MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Protein and Peptide Letters' source. Wed, 17 Mar 2010 16:27:22 +0100 http://www.medworm.com/index.php?rid=3347008&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205649%26dopt%3DAbstract Authors: Okamoto DN, Kondo MY, Hiraga K, Juliano MA, Juliano L, Gouvea IE, Oda K Enzyme-substrate interaction under the presence of high concentration of salts is of great interest for biotechnology applications and basic enzymology. In our previous work, the salt effect on halophilic subtilase SR5-3 was evaluated with Suc-AAPF-MCA and with the FRET peptide Abz-AAPFSSKQ-EDDnp. It was demonstrated that the magnitude of catalytic activity enhancement was affected by the presence of the prime site residues (Okamoto et al., 2009). In this work, a detailed analysis of the salt effect on SR5-3 protease substrate specificity was performed using chromogenic and coumarin substrates as well as FRET peptides derived from Abz-KLRSSKQ-EDDnp. The followings were demonstrated: 1) Preference of amino ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347008 Sat, 06 Mar 2010 00:00:00 +0100 3347008 http://www.medworm.com/index.php?rid=3347007&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205650%26dopt%3DAbstract Authors: Bayryamov SG, Vassilev NG, Petkov DD Bz(NO(2))-Orn(Boc)-OCH(2)CN was synthesized as an amino acid component with effective and successful orthogonal protection for amino acylation of 5'-O-Pivaloyl nucleosides and preparation of substrates for model ribosome reactions. The synthesis was carried out using suitable combinations of the methods of peptide synthesis and modification of amino acids. PMID: 20205650 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347007 Sat, 06 Mar 2010 00:00:00 +0100 3347007 http://www.medworm.com/index.php?rid=3347006&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205651%26dopt%3DAbstract Authors: Sang YX, Zhang XW, Chen XJ, Xie K, Qian CW, Hong A, Xie QL, Xiong S Overactivity of platelet-derived growth factor (PDGF) has been linked to malignant cancers. High levels of PDGF result in the activation of its receptors (PDGFRs) and the over-proliferation of cells. Therefore, interfering with this signaling pathway in cancer cells could be significant for anti-cancer drug development. In a previous study, the sPDGFRalpha-Fc fusion protein expressed in static CHO-k(1) cells showed an anti-proliferative effect on vascular endothelial cells. However, it was difficult to obtain a large quantity of this fusion protein for further functional studies. In the present study, the sPDGFRalpha-Fc fusion protein was transiently expressed in Chinese Hamster Ovary (CHO) DG44 cells in 50-mL... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347006 Sat, 06 Mar 2010 00:00:00 +0100 3347006 http://www.medworm.com/index.php?rid=3347005&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205652%26dopt%3DAbstract Authors: Nebel JC, Walawage CG Studies have shown that inverse proteins are relatively abundant. In this work, we investigate the proposition that the repeat patterns they share with protein sequences explain this phenomenon. Using a new artificial set of peptide sequences which also display these features and a random set, we show that the presence of repeats contributes to protein sequence similarity. Further analysis confirms that most inverse proteins exhibit repeats. Therefore, we suggest the relative abundance of inverse proteins can be explained by the fact they display the same repeat structures and amino acid propensity of existing proteins. PMID: 20205652 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347005 Sat, 06 Mar 2010 00:00:00 +0100 3347005 http://www.medworm.com/index.php?rid=3347004&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205653%26dopt%3DAbstract Authors: Ostuni A, Miglionico R, Bisaccia F, Antonietta M, Morelli C Multidrug-resistance-associated protein 6 (MRP6/ABCC6) is a protein belonging to the ABC transporter family which couple ATP hydrolysis with the transport of molecules across biological membranes. MRP6 topology presents three transmembrane domains and two nucleotide-binding domains (NBDs). The protein is structurally and functionally poorly characterized. Mutations in ABCC6 gene cause Pseudoxanthoma elasticum, a recessive genetic disorder affecting the elastic tissues. Most mutations have been found in NBDs that are critical for ATP binding and hydrolysis. With the aim to better characterize MRP6, we have performed a preliminary study on the fragment E748-A785 of MRP6-NBD1, with the wild type sequence and the R765Q mu... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347004 Sat, 06 Mar 2010 00:00:00 +0100 3347004 http://www.medworm.com/index.php?rid=3347003&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205654%26dopt%3DAbstract Authors: Zhao J, Huang QL, Tang YH, Zhao FK, Feng YM The in vitro insulin unfolding had been studied using the "equilibrium unfolding" method where protein is unfolded by reducing reagents in the presence of trace amounts of oxidants such as oxidized glutathione. Nine intermediates were captured in the unfolding process, named as P1A, P2A, P3A, P4A, P3B, P4B, P5B, P6B, and P7B, which were all either A chain derivatives or B chain derivatives. No intermediate with inter-A-B chain disulfide was captured. Based on the character of the intermediates, their distribution during the unfolding process and the hypothetic "transient" intermediates, an in vitro putative unfolding pathway of insulin had been proposed. Besides, the comparison of the intermediates captured in unfolding with the inte... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347003 Sat, 06 Mar 2010 00:00:00 +0100 3347003 http://www.medworm.com/index.php?rid=3347002&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205655%26dopt%3DAbstract Authors: Xie W, Blain KY, Kuo MM, Choe S Two-component systems (TCS) involving the His-Asp phosphotransfer are commonly utilized for signal transduction in prokaryotes in which the two essential components are a sensor histidine kinase (HK) receptor and a response regulator (RR). Despite great efforts in structural and functional characterization of signal perception mechanisms, the exact signaling mechanisms remain elusive for many TCSs. Mimicking the natural TCS signaling pathways, chimeric receptor kinases and response regulators have been constructed through the process of swapping modular domains of related TCSs. To design chimeras with new signaling pathways, domains from different proteins that have little relationship at the primary structural level but carrying desirable funct... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347002 Sat, 06 Mar 2010 00:00:00 +0100 3347002 http://www.medworm.com/index.php?rid=3347001&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205656%26dopt%3DAbstract Authors: Mollica A, Feliciani F, Stefanucci A, Cacciatore I, Cornacchia C, Torino D, Pinnen F It has been recently reported that thiol groups could play an important role in the protection of neuronal cells in Alzheimer's disease (AD), prion disease (CJD) and Parkinson's disease (PD). Also bucillamine, that is a pseudo dipeptide possessing a thiol group capable to form an internal disulfide bridge, has relevant scavenger properties used in therapy for the treatment of arthritis. Also furthermore, many sulphur containing compounds show strong chelating properties to heavy metals. Due to the crucial role of thiol groups in a variety of detoxicant biological systems, we report the synthesis of a racemic beta,beta-dialkylsubstituted, fully protected, cysteine derivative as a suitable inter... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347001 Sat, 06 Mar 2010 00:00:00 +0100 3347001 http://www.medworm.com/index.php?rid=3347000&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205657%26dopt%3DAbstract In this study, we have developed a standalone tool called as ANAMBS (Analysis of Metal Binding Site) to derive metal neighbourhood information using PERL as the programming language. The tool accepts the structures in the pdb format. The cut off distance to define the metal binding region can be specified. The metal binding site composition, orientation of various amino acids and atoms along with the Hydropathy index within the metal binding site region can be measured. Its speed and efficiency makes it a beneficial tool for various structural biology projects, especially when the characterization of the metal binding domain is needed. Additionally, the database MEDB (Metal Environment Database) was developed which presents quantitative information on metal-binding sites in protein structu... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3347000 Sat, 06 Mar 2010 00:00:00 +0100 3347000 http://www.medworm.com/index.php?rid=3346999&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20205658%26dopt%3DAbstract Authors: Li RF, Li H Taking all the proteins of four virus genomes as samples, the segments of alpha-helix and beta-strand in proteins of the four viruses were obtained. Linear regression analyses between the average polarities and the folding rates of peptide chains were performed for alpha-helices and beta-strands respectively. The results indicated that the folding rates show significant positive linear correlation for alpha-helices and negative linear correlation for beta-strands with the average polarities. Based on the corresponding protein coding sequences of these amino acid segments, the influences of GC content of palindromes and palindrome densities in protein coding segments on the relations between the folding rates and the average polarities were studied. Results showed t... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3346999 Sat, 06 Mar 2010 00:00:00 +0100 3346999 http://www.medworm.com/index.php?rid=3284539&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156182%26dopt%3DAbstract Authors: Wang Q, Xu F, Mou J, Zhang J, Shang L, Luan Y, Yuan Y, Liu Y, Li M, Fang H, Wang B, Xu W A novel class of L-lysine derivatives as aminopeptidase N (APN) inhibitors was designed and synthesized. Activity evaluation showed that compound C7 (IC(50) = 9.6 +/- 1.3 microM) and C20 (IC(50) = 13.6 +/- 1.9 microM) were equivalent to the positive control Bestatin (IC(50) = 11.3 +/- 1.6 microM). PMID: 20156182 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284539 Tue, 16 Feb 2010 00:00:00 +0100 3284539 http://www.medworm.com/index.php?rid=3284538&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156183%26dopt%3DAbstract Authors: El-Fakharany EM, Haroun BM, Ng TB, Redwan ER There is no protective vaccine or effective drug against hepatitis C virus (HCV). Sustained virological response to INF/ribavirin treatment regimen has an efficiency of about 50%. Many patients worldwide have used traditional medicines and herbal medicine in particular. A laccase has been purified from oyster mushroom (Pleurotus ostreatus) to homogeneity by DEAE Affi-gel blue gel, CM-Sephadex G-50 and Sephadex G-100. The molecular weight of the laccase was about 58 kDa in SDS-PAGE. The optimum pH and temperature of the laccase activity were pH 4.0 and 60 degrees C, respectively. The activity of the enzyme increased steadily from 20 to 40 degrees C, then very slowly from 40 degrees to 60 degrees C, while the enzyme activity decreased... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284538 Tue, 16 Feb 2010 00:00:00 +0100 3284538 http://www.medworm.com/index.php?rid=3284537&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156184%26dopt%3DAbstract In this study, after soluble expression, single-step purification and conversion to active protease, it was applied for the screening secretory metalloproteinase inhibitors in conditioned media of human cancer cells. PMID: 20156184 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284537 Tue, 16 Feb 2010 00:00:00 +0100 3284537 http://www.medworm.com/index.php?rid=3284536&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156185%26dopt%3DAbstract Authors: Afroz A, Khan MR, Komatsu S Jasmonic acid (JA) and salicylic acid (SA) are signaling molecules that play key roles in the regulation of metabolic processes, reproduction, and defense against pathogens. The proteomics approach was used to identify proteins that are induced by JA and SA in the tomato cultivars Roma and Pant Bahr, which are susceptible and resistant to bacterial wilt, respectively. Threonine deaminase and leucine amino peptidase were upregulated, and ribulose-1,5-bisphosphate carboxylase/oxygenase small chain was downregulated by time-course application of JA. Translationally controlled tumor protein was upregulated by time-course application of SA. Protein disulfide isomerase was upregulated by application of either JA or SA. Proteins related to defense, energy,... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284536 Tue, 16 Feb 2010 00:00:00 +0100 3284536 http://www.medworm.com/index.php?rid=3284535&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156186%26dopt%3DAbstract Authors: Li WY, Chen FF, Song C, Gao NY The non-covalent interaction of reactive brilliant red (RBR) as a representative of sulfonic azo compounds with human serum albumin (HSA) was investigated by a combination of UV-VIS spectrometry, fluorophotometry, circular dichroism (CD) and isothermal titration calorimetry (ITC) technique. The thermodynamic characterization of the interaction was performed. The saturation binding numbers of RBR on peptide chains were determined and the effects of electrolytes and temperature were investigated. The ionic interaction induced a combination of multiple non-covalent bonds including hydrogen bonds, hydrophobic interactions and van der Waals force. A three-step binding model of RBR was revealed by ITC studies. The binding of RBR molecules might occur o... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284535 Tue, 16 Feb 2010 00:00:00 +0100 3284535 http://www.medworm.com/index.php?rid=3284534&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156187%26dopt%3DAbstract Authors: Buchko GW The crystal structure for the Deinococcus radiodurans Nudix protein DR_0079 was recently determined in the metal-free form at 1.9 A resolution (2O5F). The protein adopts the fundamental fold common to the Nudix family of proteins, a large mixed b-sheet sandwiched between the a-helix of the "Nudix box" and a second a-helix. The protein's physical properties were further characterized by circular dichroism (CD) spectroscopy. A CD thermal melt at 220 nm indentifies an inflection point at approximately 52 degrees C. However, unlike typical CD thermal melts, the negative ellipticity at 220 nm becomes more negative upon passing through the inflection point. Both NMR spectroscopy and size exclusion chromatography indicate that heating effects the irreversible formation of a... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=3284534 Tue, 16 Feb 2010 00:00:00 +0100 3284534 http://www.medworm.com/index.php?rid=2751821&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19715533%26dopt%3DAbstract In this study, a 48-kDa lectin (KBL) was purified from Korean large black soybeans using liquid chromatography. The specific hemagglutinating activity of the KBL was 4096 titer/mg. EDTA-induced loss of hemagglutinating activity of KBL could be recovered by addition of Fe(3+) ions and some divalent cations as Ca(2+), Mn(2+), Fe(2+), Cu(2+), Zn(2+), and Pb(2+). Sugars such as D-(+)-galactose, D-(+)-raffinose, L-(+)-arabinose, alpha-D-(+)-melibiose, and alpha-lactose could inhibit the hemagglutinating activity of the lectin. Furthermore, the protein showed high thermal stability as well as stability over a wide range of pH values. KBL inhibited HIV-1 reverse transcriptase activity with an IC(50) of 1.38 microM. However, it was destitute of cytokine releasing, mitogenic, ribonuclease and antif... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2751821 Tue, 01 Sep 2009 14:10:05 +0100 2751821 http://www.medworm.com/index.php?rid=2668313&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19645687%26dopt%3DAbstract Authors: Shi R, Hu X Based on enzyme sequence, using composite vectors with amino acid composition, low-frequency power spectral density, increment of diversity by combining a different form of pseudo amino acid composition to express the information of sequence, a support vector machine (SVM) for predicting enzyme subclasses is proposed. By the jackknife test, success rates of our algorithm are higher than other methods. PMID: 19645687 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2668313 Tue, 04 Aug 2009 23:18:08 +0100 2668313 http://www.medworm.com/index.php?rid=2668312&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19645688%26dopt%3DAbstract This study highlights the ribosomal display technology for the selection of human antibody from patient-derived gene pools. PMID: 19645688 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2668312 Tue, 04 Aug 2009 23:18:05 +0100 2668312 http://www.medworm.com/index.php?rid=2602589&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19594430%26dopt%3DAbstract Authors: Kahle NA, Joffroy C, Popp SL, Knabbe C, Stope MB To investigate the processing of transforming growth factor beta1 (TGFbeta1) pro-protein by furin protease we expressed a GST-pro-TGFbeta1 fusion protein in bacteria. Analysis of the furin digestion pattern revealed the liberation of 12.5 kDa TGFbeta1 monomers. There was no evidence for cleavage of an alternative furin site within the pro-protein. PMID: 19594430 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2602589 Wed, 15 Jul 2009 16:10:11 +0100 2602589 http://www.medworm.com/index.php?rid=2602588&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19594431%26dopt%3DAbstract Authors: Gu Q, Ding YS, Zhang TL We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method. Compared with the results reported, the successful rate is encouraging. The source code is written by Matlab. PMID: 19594431 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2602588 Wed, 15 Jul 2009 16:10:09 +0100 2602588 http://www.medworm.com/index.php?rid=2602587&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19594432%26dopt%3DAbstract Authors: Duus K, Sandhu N, Jørgensen CS, Hansen PR, Steinø A, Thaysen-Andersen M, Højrup P, Houen G The interaction of calreticulin with native and denatured forms and polypeptides in proteolytic digests of proteins representing structural classes of all-alpha-helix (hemoglobin, serum albumin), all-beta-sheet (IgG) and alpha-helix + beta-sheets (lysozyme, ovalbumin) was investigated. The binding of calreticulin to denatured proteins was found to depend on conformation and structural class of the protein. No interaction was observed with the native proteins, whereas binding was seen for the denatured proteins, the order of interaction being lysozyme = IgG > ovalbumin >> hemoglobin = serum albumin. Moreover, the interaction between calreticulin and the heat-denatu... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2602587 Wed, 15 Jul 2009 16:10:07 +0100 2602587 http://www.medworm.com/index.php?rid=2602586&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19594433%26dopt%3DAbstract Authors: Eugenio S, Caoili C Benchmarking B-cell epitope prediction for vaccine design is meaningful if based on empirical reference data pertaining to cross-reactivities of antipeptide antibodies with native protein antigens; yet it is complicated by such data acquired using antibodies raised against peptide-protein conjugates, as peptide-protein conjugation can differentially suppress antibody responses to peptide epitopes. PMID: 19594433 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2602586 Wed, 15 Jul 2009 16:10:05 +0100 2602586 http://www.medworm.com/index.php?rid=2546436&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508177%26dopt%3DAbstract Authors: Wolf IV, Meinardi CA, Zalazar CA The milk fat is an essential component for the development of correct flavour in cheese. The lipolysis and catabolism of fatty acids are two biochemical events very important on flavour development of some cheese varieties. The role and characteristics of various lipolytic agents during cheese ripening is reviewed and discused. PMID: 19508177 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546436 Sun, 28 Jun 2009 03:45:37 +0100 2546436 http://www.medworm.com/index.php?rid=2546434&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508178%26dopt%3DAbstract Authors: Chahinian H, Sarda L Carboxylesterases (Carboxyl ester hydrolase) include two groups of enzymes, namely non-specific esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3) which have been early differentiated on the basis of their substrate specificity. Esterases hydrolyse solutions of water-soluble short acyl chain esters and are inactive against water-insoluble long chain triacylglycerols which, in turn, are specifically hydrolyzed by lipases. Based on the comparison of the primary structures, three families of sequence-related carboxylesterases, namely the lipoprotein lipase family (L-family), the hormone-sensitive lipase family (H-family) and the cholinesterase family (C-family) have been identified. Using solutions and emulsions of vinyl, glyceryl and p-nitrophenyl esters, we ha... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546434 Sun, 28 Jun 2009 03:45:34 +0100 2546434 http://www.medworm.com/index.php?rid=2546432&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508179%26dopt%3DAbstract Authors: Manco G, Nucci R, Febbraio F The quest for a quick and easy detection of the neurotoxin levels in the environment has fostered the search for systems alternative to currently employed analytical methods such as spectrophotometer, gas-liquid chromatography, thin-layer chromatography, and more recently mass spectrometry. These drawbacks lead to intense research efforts to develop biosensor devices for the determination of these compounds. In this review, we present an overview of the actual development of research in neurotoxin detection by using enzymatic biosensors based on esterase activity, in particular cholinesterases, and carboxylesterases. Detection by enzymatic activity could be carried out measuring the hydrolysis products or the residual enzymatic activity after inhib... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546432 Sun, 28 Jun 2009 03:45:32 +0100 2546432 http://www.medworm.com/index.php?rid=2546430&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508180%26dopt%3DAbstract Authors: Masson P, Carletti E, Nachon F Human butyrylcholinesterase (BuChE) is a serine enzyme present in most organs and plasma. No clear physiological function has yet been assigned to BuChE, but it is a pharmacologically and toxicologically important enzyme that plays a role in degradation of numerous ester-containing drugs and poisonous esters. Thus, BuChE-based bioscavengers are an alternative for prophylaxis and treatments of intoxications by these compounds. Also, BuChE has been integrated in biosensors for detection of organophosphorus compounds and other cholinesterase inhibitors. PMID: 19508180 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546430 Sun, 28 Jun 2009 03:45:29 +0100 2546430 http://www.medworm.com/index.php?rid=2546428&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508181%26dopt%3DAbstract Authors: Sanghani SP, Sanghani PC, Schiel MA, Bosron WF Carboxylesterases belong to Phase I group of drug metabolizing enzymes. They hydrolyze a variety of drug esters, amides, carbamates and similar structures. There are five 'carboxylesterase' genes listed in the Human Genome Organization database. In this review, we will focus on the CES1, CES2 and CES3 genes and their protein products that have been partially characterized. Several variants of these three CESs result from alternate splicing, single nucleotide polymorphisms and multiple copy variants. The three CESs, are largely localized to tissues that are major sites of drug metabolism like the mucosa of the gastrointestinal tract, lungs and liver but, they differ in tissue-specific expression. The amino acid alignment of the thr... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546428 Sun, 28 Jun 2009 03:45:27 +0100 2546428 http://www.medworm.com/index.php?rid=2546426&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508182%26dopt%3DAbstract Authors: Del Vecchio P, Graziano G, Barone G In the last years we have performed a series of studies to characterize the conformational stability of three esterases from thermophilic and mesophilic sources: Aes esterase from Escherichia coli, EST2 from Alicyclobacillus acidocaldarius and AFEST from Archeoglobus fulgidus. These three esterases belong to the Hormone-sensitive lipase group of the superfamily of carboxylester hydrolases. The conformational stability of the three enzymes against temperature, urea and GuHCl has been determined by means of circular dichroism, fluorescence and differential scanning calorimetry measurements. Analysis of experimental data coupled with available structural information allowed us to suggest that the optimization of charge-charge interactions on th... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546426 Sun, 28 Jun 2009 03:45:25 +0100 2546426 http://www.medworm.com/index.php?rid=2546424&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508183%26dopt%3DAbstract Authors: Mandrich L, Merone L, Manco G Thermophilic and hyperthermophilic carboxylesterases (EC 3.1.1.1) are excellent model systems for studying structure function relationships as well as in vitro and in vivo evolution and possible biotechnological applications. In this paper we review the main aspect of one of most studied microbial representative of the hormone sensitive lipase family (HSL), namely carboxylesterase 2 (EST2) from Alicyclobacillus acidocaldarius. PMID: 19508183 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546424 Sun, 28 Jun 2009 03:45:22 +0100 2546424 http://www.medworm.com/index.php?rid=2546422&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508184%26dopt%3DAbstract Authors: Yan S, Cui F, Qiao C Carboxylesterases (EC 3.1.1.1) distribute broadly in insects, and play an important role in the metabolism with various functions. This paper reviews the insect carboxylesterases including the definitions and reaction mechanism, classification, structural context, functions especially on insecticide resistance, and its application. PMID: 19508184 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546422 Sun, 28 Jun 2009 03:45:20 +0100 2546422 http://www.medworm.com/index.php?rid=2546420&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508185%26dopt%3DAbstract Authors: Tutino ML, di Prisco G, Marino G, de Pascale D Micro-organisms that thrive at low temperatures produce cold-adapted enzymes which display high catalytic efficiency, generally associated with low thermal stability. In the recent past, researchers and industries have focused the attention on cold-adapted enzymes, whose peculiar properties make them particularly interesting either for investigating stability/flexibility relationships, or for their potential application in industrial processes. Among these enzymes, lipases and esterases, have potential utilisations in a broad range of biotechnological applications. In fact, these biocatalysts represent the most widely used enzymes in biotechnology and organic chemistry. Modern methods of genetic engineering combined with growing k... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546420 Sun, 28 Jun 2009 03:45:17 +0100 2546420 http://www.medworm.com/index.php?rid=2546418&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508186%26dopt%3DAbstract Authors: Schmidt M, Böttcher D, Bornscheuer UT In the past few years a considerable number of mutagenesis methods and high-throughput screening (HTS) systems have been developed and improved. In parallel computer programs or software packages for molecular modeling have be further investigated. Thus, the number of examples for successful directed evolution and rational design is increasing constantly. In this review the essential mutagenesis methods and HTS systems, especially for esterases, are described and various examples for the application of these protein engineering tools are provided. PMID: 19508186 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546418 Sun, 28 Jun 2009 03:45:15 +0100 2546418 http://www.medworm.com/index.php?rid=2546416&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508187%26dopt%3DAbstract Authors: Carr PD, Ollis DL The alpha/beta hydrolase superfamily has rapidly expanded in recent years and continues to do so at an expeditious pace. According to the ESTHER database (http://bioweb.ensam.inra.fr/ESTHER) 29000 papers have been published cataloguing 89 family groups, comprising a total of 15438 gene loci and 666 structures. This paper presents a snapshot of the current family taxonomy, catalytic chemistries, structural topologies and useful technologies emerging from the knowledge base at the current time. PMID: 19508187 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546416 Sun, 28 Jun 2009 03:45:13 +0100 2546416 http://www.medworm.com/index.php?rid=2546414&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508188%26dopt%3DAbstract Authors: Pohanka M, Musilek K, Kuca K Aflatoxins are group of secondary metabolites from moulds. The main toxic effect of alfatoxins on body is based on metabolic activation on cytochrome P450 system. Recently, some studies appointed at anticholinergic properties of aflatoxins and inhibition of acetylcholinesterases (AChE) was described. Inhibition is reversible; however, some questions arose. Is the interaction firmly enough to prevent distribution of aflatoxins in body? Could be AChE considered as a scavenger of aflatoxins? Amperometric biosensor with immobilized acetylcholinesterase was used for evaluation of aflatoxin B1 (AFB1) - AChE complex spontaneous dissociation, where AFB1 acts as an inhibitor. Displacement of solution with substrate and AFB1 by the intact one enabled estimat... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546414 Sun, 28 Jun 2009 03:45:10 +0100 2546414 http://www.medworm.com/index.php?rid=2546412&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508189%26dopt%3DAbstract Authors: Macedo ML, Pando SC, Chevreuil LR, Marangoni S DrTI was effective against trypsin-like enzymes from A. kuehniella and C. cephalonica, however an artificial diet was insufficient to affect the survival and body weight of either insect. The inhibitor stimulated chymotrypsin-like enzymes and probably induced the synthesis of enzymes insensitive to TLCK in neonate larvae. PMID: 19508189 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546412 Sun, 28 Jun 2009 03:45:08 +0100 2546412 http://www.medworm.com/index.php?rid=2546410&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508190%26dopt%3DAbstract Authors: Wang C, Sha Y We used a de novo designed, beta-hairpin forming T1 peptide as a model to investigate the kinetics of peptide fibrogenesis by a combination of light scattering (LS), circular dichroism (CD), fluorescence, and atomic force microscopy (AFM). The results demonstrate that the T1 fibrogenesis undergoes a consecutive stepwise process, with a high degree of cooperation, presenting sigmoidal time-courses of the peptide aggregation, the subsequent conformational conversion of the backbone, and the peptide sidechains' rearrangement. We suggest that the conformational conversion was initiated after the peptide aggregates reach a dimensional size threshold, which could be a key step in the formation of beta-structural nuclei that catalyze the subsequent reactions. Furthermor... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546410 Sun, 28 Jun 2009 03:45:05 +0100 2546410 http://www.medworm.com/index.php?rid=2546409&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508191%26dopt%3DAbstract Authors: Xu Z, Lian J, Cai J Aquaporin Z (AqpZ) is a typical orthodox aquaporin with 6 transmembrane domains and five connecting loops. In order to express this complex membrane protein efficiently, E. coli cell-free expression system was employed as an alternative to produce aquaporin Z. Using different fusion vectors containing AqpZ gene, the expression level of fusion proteins in cell-free system varied from 7.97 to 578.35 microg/ml, while 7.34 to 340.81 microg/ml for target protein (AqpZ). The free energy of mRNA secondary structure at translation initiation region (TIR) was predicted and demonstrated a positive relationship with the expression level of AqpZ in cell-free system. This is the first report of expressing water channel protein in E. coli cell-free system, which has beco... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546409 Sun, 28 Jun 2009 03:45:03 +0100 2546409 http://www.medworm.com/index.php?rid=2546408&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508192%26dopt%3DAbstract Authors: Miyazawa T, Hamada T Dynamic kinetic resolution (DKR) was demonstrated in the carbodiimide-mediated couplings of N-benzoyl-DL-amino acids with L-amino acid esters: the yields of the D-L-peptides significantly exceeded 50% in some cases. N-Benzoyl-DL-t-leucine afforded the D-L-peptide almost exclusively (up to 96% yield) in the reaction with methyl L-prolinate, which is the most efficient DKR obtained in the field of amino acids and derivatives. PMID: 19508192 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546408 Sun, 28 Jun 2009 03:45:01 +0100 2546408 http://www.medworm.com/index.php?rid=2546407&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508193%26dopt%3DAbstract Authors: Cannio R, Catara G, Fiume I, Balestrieri M, Rossi M, Palmieri G A new protease, named SsMTP was identified from the archeon Sulfolobus solfataricus. The enzyme is associated to the cell-membrane and over-produced in response to the peptide-enriched media. SsMTP has a molecular mass of 120 kDa showing optimal activity at pH 2.0 in the temperature range 70 - 90 degrees C, and a half-life of 20 days at 80 degrees C. Primary structure analysis revealed that SsMTP represents a novel type of multi-domain thermopsin-like protease containing the catalytic domain followed by two distinct domains, PKD and Y_Y_Y, which are usually involved in a range of protein-protein interactions among the extracellular proteins. PMID: 19508193 [PubMed - as supplied by publisher] (Source: Protein a... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546407 Sun, 28 Jun 2009 03:44:59 +0100 2546407 http://www.medworm.com/index.php?rid=2546406&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508194%26dopt%3DAbstract Authors: Rajasekaran R, Rao S We analyzed 27 antifungal peptides (AFPs) to understand their stability by various parameters like, stabilization centers, GROMOS, OPLS and FOLDEF force fields. Subsequently, we propose that AFP, NK-Lysin could be considered a potential candidate and also could act as a template for designing the therapeutic peptide drug against pathogenic fungi. PMID: 19508194 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546406 Sun, 28 Jun 2009 03:44:57 +0100 2546406 http://www.medworm.com/index.php?rid=2546405&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508195%26dopt%3DAbstract Authors: Himmerich H, Sheldrick AJ Tumor necrosis factor-alpha (TNF-alpha) is a glycoprotein hormone with important functions in inflammation and apoptosis. It plays a significant role as a pro-inflammatory cytokine in the defense against viral, bacterial and parasitic infections and autoimmune disorders. Furthermore, it influences energy homeostasis and has an anorexigenic effect on the hypothalamus. TNF-alpha has also been shown to be involved in the pathogenesis of psychiatric disorders such as depression or narcolepsy. Ghrelin is a peptide hormone which primarily regulates eating behavior through modulation of expression of orexigenic peptides in the hypothalamus. Ghrelin administration increases food intake and body weight, while weight loss in turn increases ghrelin levels. Secon... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546405 Sun, 28 Jun 2009 03:44:55 +0100 2546405 http://www.medworm.com/index.php?rid=2546404&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508196%26dopt%3DAbstract We report a one pot synthesis of Fmoc amino acid derived 4-amino-thiazole derivatives and thiazole linked N-orthogonally protected dipeptidomimetics by the condensation of N(alpha)-Fmoc alpha-halomethylketones with thiourea and Boc/Z-alpha-amino acid thioamides via modified Hantzch protocol. Side chain modified Fmoc amino acids containing 4-amino thiazole moiety have also been synthesized following the similar protocol. PMID: 19508196 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546404 Sun, 28 Jun 2009 03:44:53 +0100 2546404 http://www.medworm.com/index.php?rid=2546403&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508197%26dopt%3DAbstract Authors: Wong JH, Ng TB An antifungal protein with multiple stable biological activities unaffected by chemical modification of tyrosine and tryptophan, and a protein with N-terminal sequence and molecular mass resemblance but no identifiable activities were isolated from culture broth of Bacillus amyloliquefaciens. The findings are analogous to previous reports on thaumatin and thaumatin-like proteins. PMID: 19508197 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546403 Sun, 28 Jun 2009 03:44:51 +0100 2546403 http://www.medworm.com/index.php?rid=2546402&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508198%26dopt%3DAbstract In this study, we selected six recently published methods (DISPHOS, NetPhosK, PPSP, KinasePhos, Scansite and PredPhospho) to evaluate their performance. First, we compiled three testing datasets containing experimentally verified phosphorylation sites for mammalian, Arabidopsis and rice proteins. Then, we present the prediction performance of the tested methods on these three independent datasets. Rather than quantitatively ranking the performance of these methods, we focused on providing an understanding of the overall performance of the predictors. Based on this evaluation, we found the following results: i) current phosphorylation site predictors are not effective for practical use and there is substantial need to improve phosphorylation site prediction; ii) current predictors perform p... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546402 Sun, 28 Jun 2009 03:44:49 +0100 2546402 http://www.medworm.com/index.php?rid=2546401&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508199%26dopt%3DAbstract Authors: Cong Z, Huang Y, Yang L, Ye D, Dong S The photo-switchable insect kinin thioxo-analog Phe(1)-Tyr(2)-Psi[CS-N]-Pro(3)-Trp(4)-Gly(5)-NH(2) (Psi[CS-N](2)-Kinin) can change from ground state to photo-stationary state by following a pulse of UV radiation and its bioactivity increases simultaneously. To investigate the conformation-activity relationship, the solution structure of its ground state was determined by two-dimensional NMR spectroscopy. In contrast, the photo-stationary state could not be determined because of its relatively fast thermal reisomerization. The molecular dynamics-calculated structures based on NMR constraints demonstrate that the trans Pro conformer is the predominant conformation for the ground state in aqueous solution, which was also confirmed by the very... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546401 Sun, 28 Jun 2009 03:44:47 +0100 2546401 http://www.medworm.com/index.php?rid=2546400&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508200%26dopt%3DAbstract Authors: Kishan KV, Sharma A Proteases have been used not only for proteolysis but also in organic solvent-assisted religation processes. Here, we demonstrated the effect of salts on peptide bond resynthesis in Glutathione-S-transferase (GST) and have found it to be in the purview of the Hofmeister phenomena. Our results show that the efficiency and ease of religation increases with an increase in the surface charge densities of the cations used in the study. Thus, the yield of religated GST follows the order: Mg2(+)>Li(+)>Na(+)>K(+). Characteristics of the salt-religated GST were studied using size exclusion chromatography, CD spectroscopy, mass spectrometry and CDNB activity assay. Results show that the properties of salt-religated GST are in close agreement with... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546400 Sun, 28 Jun 2009 03:44:45 +0100 2546400 http://www.medworm.com/index.php?rid=2546399&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508201%26dopt%3DAbstract Authors: Chen M, Yang B, Ying W, He F, Qian X A novel strategy to annotate nsSNP-peptides in human liver proteome based on LC-ESI-MS/MS and peptide database search was proposed. Totally 115 nsSNP-peptides in human liver proteins were annotated using our method. Among them, 42 peptides were found to be amino acid mutation, 73 peptides were wild type, 5 peptides were interpreted with both mutation and wild type. The function of nsSNP-peptide was predicted using SIFT algorithm, and 2 nsSNPs were predicted to be damaged for protein function. The results here show that the strategy is very effective for annotation of nsSNP at peptide level. PMID: 19508201 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546399 Sun, 28 Jun 2009 03:44:43 +0100 2546399 http://www.medworm.com/index.php?rid=2546398&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508202%26dopt%3DAbstract Authors: Li Q, Cao Z, Liu H The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546398 Sun, 28 Jun 2009 03:44:41 +0100 2546398 http://www.medworm.com/index.php?rid=2546397&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508203%26dopt%3DAbstract Authors: Wang T, Yang J With the rapid increase of protein sequences in the post-genomic age, the need for an automated and accurate tool to predict protein subcellular localization becomes increasingly important. Many efforts have been tried. Most of them aim to find the optimal classification scheme and less of them take the simplifying the complexity of biological system into consideration. This work shows how to decrease the complexity of biological system with linear DR (Dimensionality Reduction) method by transforming the original high-dimensional feature vectors into the low-dimensional feature vectors. A powerful sequence encoding scheme by fusing PSSM (Position-Specific Score Matrix) and Chou's PseAA (Pseudo Amino Acid) composition is proposed to represent the protein samples.... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546397 Sun, 28 Jun 2009 03:44:39 +0100 2546397 http://www.medworm.com/index.php?rid=2546396&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508204%26dopt%3DAbstract Authors: Thompson MW, Beasley KA, Schmidt MD, Seipelt RL A previously uncharacterized member of the M1 family of zinc metallopeptidases, arginyl aminopeptidase-like 1 (RNPEPL1; EC 3.4.11.1), was cloned and expressed, and the recombinant enzyme characterized. RNPEPL1 was a broad specificity aminopeptidase with preference for a P1 methionine, glutamine, or citrulline residue, and exhibited a broad pH preference, with maximal activity observed between pH 6.6 and 8.0. The enzyme was inhibited by calcium ions but unaffected by chloride ions, and was insensitive to specific inhibitors of the closely-related arginyl aminopeptidase, indicating similarity to leukotriene A(4) hydrolase. RT-PCR analysis of RNPEPL1 expression revealed a ubiquitous tissue distribution, consistent with a general hou... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546396 Sun, 28 Jun 2009 03:44:37 +0100 2546396 http://www.medworm.com/index.php?rid=2546395&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508205%26dopt%3DAbstract Authors: Youn K, Park C Protein inactivation frequently occurs through partially unfolded states under native conditions, and temperature is an important parameter that affects the susceptibility of proteins to inactivation. While the effect of temperature on global unfolding is well documented, however, experimental characterizations of the temperature effect on partial unfolding are rare. Proteolysis offers a valuable chance to investigate the temperature effect on partial unfolding. By investigating proteolysis kinetics, the energetics of the partially unfolded state responsible for proteolysis (the cleavable state) can be studied. E. coli ribonuclease H (RNase H) has been shown to be cleaved by thermolysin at the amide bond between Thr92 and Ala93 through partial unfolding. Using t... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546395 Sun, 28 Jun 2009 03:44:35 +0100 2546395 http://www.medworm.com/index.php?rid=2546394&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508206%26dopt%3DAbstract Authors: Chen CH, Chen MK, Jeng KC, Lung FD The growth factor receptor-bound protein Src homology 2 (Grb2-SH2) plays an important role in the oncogenic Ras signaling pathway, which involves in cell proliferation and differentiation. Therefore, the antagonist of Grb2-SH2 has become a potential target for developing anticancer agents. Recently, we discovered a peptide 1 (Fmoc-Glu-Tyr-Aib-Asn-NH(2)) with high affinity for the Grb2-SH2 domain by using surface plasmon resonance (SPR)-biosensor technology. Herein, we report the further design of the lead peptide 1 by addition of an Arg-Gly-Asp sequence to 1 to enhance binding to Grb2-SH2 and inducing apoptosis in cancer cells. Both the linear and cyclic analogs of the newly designed compound were prepared along with an analog in which the N(... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546394 Sun, 28 Jun 2009 03:44:33 +0100 2546394 http://www.medworm.com/index.php?rid=2546393&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508207%26dopt%3DAbstract Authors: Villa-Hernández O, Hernández-Orihuela L, Del Carmen Rodríguez M, Zamudio-Zuñiga F, Castro-Franco R, Pando V, Batista CV In this work, we describe the original characterization of peptides and proteins present in the skin secretions of the Mexican amphibian Hyla eximia. To this purpose, a novel water/dark extraction method, as well as the classic electrical stimulation procedure, was applied in order to extract the skin secretion. Two novel antimicrobial peptides He-1 and He-2 were sequenced. In addition, a molecular mass fingerprint revealed more than one hundred different molecules. Eight peptides in homogeneous form were assayed against five species of bacteria. Thereafter, the peptide He-2 demonstrated high antiparasitic activity against ookinete forms o... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546393 Sun, 28 Jun 2009 03:44:31 +0100 2546393 http://www.medworm.com/index.php?rid=2546392&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508208%26dopt%3DAbstract Authors: Thireou T, Atlamazoglou V, Papandreou NA, Lonquety M, Chomilier J, Eliopoulos E The MIR algorithm provides an ab initio prediction of a protein's core residues. An improved version, the MIR2, is presented and validated on 3203 proteins from PDB. Structures are decomposed in Closed Loops, their limits constituting the observed core residues. They are predicted by MIR2 with an accuracy approaching 80%. PMID: 19508208 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546392 Sun, 28 Jun 2009 03:44:29 +0100 2546392 http://www.medworm.com/index.php?rid=2546391&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508209%26dopt%3DAbstract Authors: Echemendia-Blanco D, Van Driessche E, Ncube I, Read JS, Beeckmans S From 1 kg of defatted Pterocarpus angolensis (mukwa tree) seed meal, 21.6 grams of an alpha,D-mannose/glucose-specific lectin can be purified on mannose-Sepharose. Relative affinities for several (oligo)saccharides and glycoproteins were studied by haemagglutination-inhibition. Gel filtration shows that the lectin exists as a dimer above pH 5 and as a monomer below pH 3.5. This is confirmed by studies on the release of lectin subunits that were adsorbed from solution to lectin monomers immobilized onto Eupergit-c. From the gel filtration patterns it is calculated that a residue with pK(a) of about 4.4 is involved in dimer dissociation. Titration of glutamic acids (E60, E209) is postulated to be involved. CD sp... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546391 Sun, 28 Jun 2009 03:44:28 +0100 2546391 http://www.medworm.com/index.php?rid=2546390&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508210%26dopt%3DAbstract Authors: Yang J Comparison between the BAD complexes indicated that BAD all docks a hydrophobic surface of PKAc regardless of its phosphorylation. PKAc may prevent Bcl-xL from rebinding to BAD by phosphorylating human BAD at Ser118; whereas human BAD is phosphorylated on Ser75 in a BAD-Bcl-xL complex, resulting in the dissociation of BAD. PMID: 19508210 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546390 Sun, 28 Jun 2009 03:44:26 +0100 2546390 http://www.medworm.com/index.php?rid=2546389&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508211%26dopt%3DAbstract Authors: Jiang XF, Yang J A protein domain interaction prediction program was complied using C(++) to predict whether a query protein could interact with other hub proteins. It is indicated that the proteins interacting with AATF (Apoptosis-Antagonizing Transcription Factor) possess a common conservative pattern: I-x(0,1)-E-x(2)-[A/E/N/T]-x-[E/K]. Our method is attempted to integrate the characteristics of protein interaction network with the simplest building blocks-conservative patterns. PMID: 19508211 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546389 Sun, 28 Jun 2009 03:44:24 +0100 2546389 http://www.medworm.com/index.php?rid=2546388&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508212%26dopt%3DAbstract Authors: Afroz A, Hashiguchi A, Khan R, Komatsu S The functions of organs in young soybean seedling were determined by means of proteomic analysis. Extracts from leaves, hypocotyls, and roots were separated by two-dimensional polyacrylamide gel electrophoresis, and the proteins were identified by mass spectrometry and protein sequencing. The identified proteins were categorized into various groups according to their function. The leaf was abundant in proteins associated with energy production (50.0%), the hypocotyl was rich in defense proteins (31.8%), and the root contained defense-related proteins (16.7%) and destination and storage proteins (26.7%). Stem 31-kDa glycoprotein, 20 kDa chaperonin, 50S ribosomal protein, and trypsin inhibitor were common to all three tissues. The sequenc... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546388 Sun, 28 Jun 2009 03:44:22 +0100 2546388 http://www.medworm.com/index.php?rid=2546387&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508213%26dopt%3DAbstract Authors: Cruz LP, Ribeiro SF, Carvalho AO, Vasconcelos IM, Rodrigues R, Da Cunha M, Gomes VM The aims of this study were to isolate and characterize peptides present in chilli pepper seeds and evaluate their antifungal activities. An isolated peptide closer to 9 kDa showed high sequence homology to the antimicrobial peptide lipid transfer protein. The peptide fraction containing the LTP inhibited the growth of the fungi, Fusarium oxysporum, Colletotrium lindemunthianum, the yeasts, Saccharomyces cerevisiae, Pichia membranifaciens, Candida tropicalis, Candida albicans, inhibited glucose-stimulated acidification of the medium by yeast cells of S. cerevisiae and caused several morphological changes in P. membranifaciens. PMID: 19508213 [PubMed - as supplied by publisher] (Source: Prot... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546387 Sun, 28 Jun 2009 03:44:20 +0100 2546387 http://www.medworm.com/index.php?rid=2546386&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508214%26dopt%3DAbstract Authors: Huang ZR, Zhu TY, Wang TT, Wang XN, Yang J Some pentapeptides with higher alpha-helical tendency possess typical sequence pattern, such as "+ - + + - - +", "+ - - + - - +", "+ - + - - - +", and "- + + - - - +" ( "+" = D,N,E,Q,K,R,T,C, or H; "-" = L,I,V, or A), especially symmetrical motifs (a pair of reverse sequences beside palindromic segments), such as ALALA, QQAQE/EQAQQ, and REALE/ELAER, hint that the nascent peptide can fold a certain conformation in a two-way folding fashion. PMID: 19508214 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546386 Sun, 28 Jun 2009 03:44:18 +0100 2546386 http://www.medworm.com/index.php?rid=2546385&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508215%26dopt%3DAbstract Authors: Shishkov AV, Bogacheva EN, Dolgov AA, Chulichkov AL, Knyazev DG, Fedorova NV, Ksenofontov AL, Kordyukova LV, Lukashina EV, Mirsky VM, Baratova LA The first attempt has been made to suggest a model of influenza A virus matrix M1 protein spatial structure and molecule orientation within a virion on the basis of tritium planigraphy data and theoretical prediction results. Limited in situ proteolysis of the intact virions with bromelain and surface plasmon resonance spectroscopy study of the M1 protein interaction with lipid coated surfaces were used for independent confirmation of the proposed model. PMID: 19508215 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546385 Sun, 28 Jun 2009 03:44:16 +0100 2546385 http://www.medworm.com/index.php?rid=2546384&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508216%26dopt%3DAbstract Authors: Chen Z, Chang M, Peng Y, Zhao L, Zhan Y, Wang L, Wang R In neonatal rat metatarsal organ culture, a bell-shaped dose-related curve in length of mineralized area, increases in the height of proliferative and hypertrophic zones, in the number of hypertrophic chondrocyte and in the amount of Runx2 mRNA, were revealed after treatment with OGP(10-14). We conclude that OGP(10-14) accelerates bone growth. PMID: 19508216 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546384 Sun, 28 Jun 2009 03:44:13 +0100 2546384 http://www.medworm.com/index.php?rid=2546383&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508217%26dopt%3DAbstract Authors: Nadeem H, Rashid MH, Riaz M, Asma B, Javed MR, Perveen R Here we report for the first time heat of ionization of invertase (E.C.3.2.1.26) active site residues from hyper-producer strain of Aspergillus niger (34.1 U ml(-1)), along with its physiochemical properties, kinetics and thermodynamics of stability-function. The Invertase showed great potential for industry as being highly efficient (k(cat) = 24167 s(-1) at 65 degrees C, pH 5.0) and stable (half life= 12 h at 56 degrees C). PMID: 19508217 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546383 Sun, 28 Jun 2009 03:44:11 +0100 2546383 http://www.medworm.com/index.php?rid=2546382&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508218%26dopt%3DAbstract Authors: Ribeiro ES, Uchôa AF, da Silva LG, Beghini DG, Ferreira AT, Perales J, Fernandes KV, Jacinto T, Xavier-Filho J, Oliveira AE An insulin-binding protein was isolated from Canavalia ensiformis seed coat, by using an insulin-Sepharose 4B affinity chromatography, and the protein was identified as canavalin (Canavalia 7S globulin) by mass spectrometry analysis. The major novelty of these data is the acidic nature of this globulin insulin-binding, in contrast to the basic Bg-like insulin-binding proteins so far reported in plants. PMID: 19508218 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546382 Sun, 28 Jun 2009 03:44:09 +0100 2546382 http://www.medworm.com/index.php?rid=2546381&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508219%26dopt%3DAbstract Authors: Kar S, Dutta A, Drew MG, Koley P, Pramanik A Single crystal X-ray diffraction studies and solvent dependent (1)H NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L-amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4-->1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning electron microscopic (FE-SEM) images of the tetrapeptides in the solid state reveal that they can form flat tape-like... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546381 Sun, 28 Jun 2009 03:44:07 +0100 2546381 http://www.medworm.com/index.php?rid=2546380&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508220%26dopt%3DAbstract Authors: Shymanets A, Ahmadian MR, Nürnberg B G-protein betagamma dimers are prime regulators transmitting extracellular signals to wide-ranging cellular effectors including phosphoinositide 3-kinase (PI3K) isoforms beta and gamma. Recombinant Gbetagamma purified from Sf9 cells via metal-affinity and anion exchange chromatography exhibited a wortmannin-insensitive phospholipid kinase activity that copurified from the insect cells. To exclude false-positive results of Gbetagamma-dependent lipid kinase activity, the elimination of insect phospholipid kinase from Gbetagamma protein samples is necessary to avoid interference with the intrinsic lipid kinase activity of PI3K isoforms in reconstitution experiments. Here we describe an improved procedure of Gbeta(1)gamma(2) purification f... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546380 Sun, 28 Jun 2009 03:44:05 +0100 2546380 http://www.medworm.com/index.php?rid=2546379&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508221%26dopt%3DAbstract Authors: Mohabatkar H, Mohsenzadeh S Since there are not much experimental data available about different structural properties of Isfahan virus (ISFV), in the present investigation, computational study of G protein of ISFV was performed and the results were compared with G proteins of Chandipura virus (CHPV) and Piry virus (PV). Calculation of amino acid compositions of G proteins of viruses was done by PseAAC server. Predictions of localization, sequence of signal peptides, C, N and O glycosylation sites, transmembrane helices, cysteine bond positions and B cell epitopes of G proteins were performed by Virus-PLoc, Signal-CF, EnsembleGly, MemBrain, DiANNA and BCPREDS servers respectively. Similarities and differences between these glycoproteins were predicted and discussed. PMID: ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546379 Sun, 28 Jun 2009 03:44:03 +0100 2546379 http://www.medworm.com/index.php?rid=2546377&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508222%26dopt%3DAbstract Authors: Mahmood T, Kakishima M, Komatsu S To study the effect of probenazole on the induced systemic resistance mechanism of rice-bacterial interaction, a proteomic approach was applied. Oryza sativa cv. Java 14 seedlings were treated with probenazole, followed by inoculation with compatible (Xo7435) and incompatible (T7174) races of Xanthomonas oryzae pv. oryzae. Cytosolic proteins were fractionated from leaf blades, separated by two-dimensional polyacrylamide gel electrophoresis. Pathogenesis-related protein 5 (PR5) was significantly induced with probenazole treatment followed by inoculation with T7174 or Xo7435. The sense PR5 transgenic rice plants were more highly resistant than the susceptible vector control against Xo7435. These results indicate that probenazole strongly induces... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546377 Sun, 28 Jun 2009 03:44:02 +0100 2546377 http://www.medworm.com/index.php?rid=2546376&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508223%26dopt%3DAbstract Authors: Choe HH, Hwang H, Kim S, Yoon S, Jo DH, Ryu Y, Kim TD A novel oligomeric decaprenyl pyrophosphate synthase was identified. Circular dichroism measurements indicated that it is alpha-helical, and stable against pH changes and denaturants. Three peptides corresponding to the conserved regions were synthesized and metal affinities were investigated. Crystallographic analyses of this oligomeric DDS are currently in progress. PMID: 19508223 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546376 Sun, 28 Jun 2009 03:44:00 +0100 2546376 http://www.medworm.com/index.php?rid=2546375&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508224%26dopt%3DAbstract Authors: Vezenkov LT, Georgieva MG, Danalev DL, Ivanov TB, Ivanova GI New analogues of galanthamine containing peptide fragments either at 6 or 11 position, were synthesized by reaction between galanthamine molecule and dipeptides and tripeptide, derivatives of N-(3,4-dichlorophenyl)-D,L-Ala-OH. The best results according to yields, easily purification of the target products, and simplicity of the scheme realisation was achieved by using of cyanomethyl ester of Boc-Gly-OH as activated compound. PMID: 19508224 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546375 Sun, 28 Jun 2009 03:43:58 +0100 2546375 http://www.medworm.com/index.php?rid=2546374&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508225%26dopt%3DAbstract Authors: Costantini S, Facchiano AM In order to study the intrinsic structural properties of three helices in human prion protein (PrP) and analyse their stability, we conducted molecular dynamics simulations, applied helix propensity predictions and evaluated the energetic contribution of the helical regions to the PrP protein stability. Our results suggest that three helices present different stability and the helix 2 results the least stable. PMID: 19508225 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546374 Sun, 28 Jun 2009 03:43:56 +0100 2546374 http://www.medworm.com/index.php?rid=2546373&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508226%26dopt%3DAbstract Authors: Saiki M, Watase M, Matsubayashi H, Hidaka Y Peptidylarginine deiminase IV (PAD4) catalyzes the conversion of an Arg residue to a citrulline residue in various proteins. In particular, citrullination of histone subunits, such as H2A and H3, by PAD4 is thought to be related to rheumatoid arthritis. However, the details of the citrullination mechanism of histone H2A and H3 are not yet well known. Moreover, the effects of N-terminal acetylation on histone subunits with respect to PAD4 recognition have not yet been studied. To further study the mechanism of PAD4 recognition of histone H2A and H3 subunits, a series of the N-terminal peptides was chemically synthesized and the citrullination sites were identified using MALDI-TOF/MS. N-terminal acetylation of histone H2A was not signi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546373 Sun, 28 Jun 2009 03:43:54 +0100 2546373 http://www.medworm.com/index.php?rid=2546372&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508227%26dopt%3DAbstract Authors: Scholz CJ, Sauer G, Deissler H We showed that Tspan-1, a tetraspanin overexpressed in many human cancers, harbours oligosaccharides at all four potential N-glycosylation sites. Its most abundant form contained only mannose-rich sugar chains but two distinct glycosylation sites could also contain complex carbohydrates. Glycosylation seemed to be required for correct folding and subsequent transition through the endoplasmic reticulum. PMID: 19508227 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546372 Sun, 28 Jun 2009 03:43:52 +0100 2546372 http://www.medworm.com/index.php?rid=2546371&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508228%26dopt%3DAbstract Authors: Chapkanov A, Miteva Y, Kolev T, Spiteller M, Koleva B The three new Au (III), Pt (II) and Pd (II) complexes with pentapeptide glycyl-glycyl-(L)-methyonyl-glycyl-glycine have been synthesized, isolated, and spectroscopically and structurally elucidated in solution and in the solid-state. Solid-state linear-dichroic infrared (IR-LD) spectroscopy of oriented colloids in a nematic liquid crystal host, (1)H- and (13)C-NMR, TGA and DSC, UV-VIS spectroscopy, EPR, ESI- and FAB- mass spectrometry and HPLC tandem mass spectrometry (HPLC-MS/MS) have been used. Quantum chemical calculations and molecular modelling were carried out in order to determine the structures and spectroscopic properties of the ligand, the newly synthesised metal complexes and their interactions with calf thymus D... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546371 Sun, 28 Jun 2009 03:43:50 +0100 2546371 http://www.medworm.com/index.php?rid=2546370&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19508229%26dopt%3DAbstract Authors: Lee L, Chen KC, Chang LS Single site-directed mutations at each of the four EF-hand loops of potassium channel-interacting protein 2.2 (KChIP2.2) were carried out to explore the functional roles of EF-hands in KChIP2.2. In contrast to those on EF-hands 1 and 2, mutations on EF-hands 3 or 4 distorted the high affinity Ca(2+)-binding site of KChIP2.2. However, the Mg(2+)-binding ability of KChIP2.2 was marginally affected by the mutations. The gross conformation of mutated KChIP2.2 was indistinguishable from wild-type KChIP2.2 as revealed by CD spectra. The results of size exclusion chromatography showed that, with exception of EF-hand 4 mutant, mutations on EF-hands 1, 2 or 3 caused KChIP2.2 to form oligomer. Pull-down assay revealed that, unlike wild-type KChIP2.2, the interac... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546370 Sun, 28 Jun 2009 03:43:48 +0100 2546370 http://www.medworm.com/index.php?rid=2546349&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19545231%26dopt%3DAbstract Authors: Gu F, Chen H To fix the large and expanding gap between sequence known proteins and structure known proteins, it is important to study on protein structural class prediction (PSCP) for its foundation and usefulness in protein structure analysis. In this paper, the d-interval conditional probability index was proposed to reflect the long-term correlation between amino acids. Based on this index, the impact of residues' long-term relationship on PSCP was analyzed. Two new information theory based algorithms were proposed and were used combining with the long-term information between residues to predict protein structural class (PSC). The dataset 5714 was tested for its low sequence similarity and high reliability. The result showed that the new index was 3-6% higher than traditi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546349 Sun, 28 Jun 2009 03:43:06 +0100 2546349 http://www.medworm.com/index.php?rid=2546470&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442222%26dopt%3DAbstract Authors: Luk JM PMID: 19442222 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546470 Sun, 28 Jun 2009 03:43:04 +0100 2546470 http://www.medworm.com/index.php?rid=2546467&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442223%26dopt%3DAbstract Authors: Doshi R, Day PJ Diseased-cell secreted proteins/peptides offer several leads in biomarker development. Blood is a rich and universal source of biomarkers because of its proximity to all cells in the body. However, important physiological and practical aspects need consideration before serum peptidomics is effectively applied in a clinical, and later bedside, setting. PMID: 19442223 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546467 Sun, 28 Jun 2009 03:43:04 +0100 2546467 http://www.medworm.com/index.php?rid=2546464&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442224%26dopt%3DAbstract Authors: Chen L, Fatima S, Peng J, Leng X The need to identify disease biomarkers is critical to ensure fast diagnosis and timely treatment. Surface enhanced laser desorption/ionization time-of-fight mass spectrometry (SELDI-TOF-MS) is a widely used technology platform for diagnostic biomarker discovery. This short review provides an overview of how it functions and also describes its advantages and drawbacks. PMID: 19442224 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546464 Sun, 28 Jun 2009 03:43:04 +0100 2546464 http://www.medworm.com/index.php?rid=2546461&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442225%26dopt%3DAbstract Authors: Sun S, Day PJ, Lee NP, Luk JM This review summarises the screening methods from hepatic ultrasonography to serological biomarkers for early detection of liver cancer and focuses on evaluation of biomarkers ability. The development of novel biomarkers according to the 5-phase program defined by the Early Detection Research Network (EDRN) is also outlined in this review. PMID: 19442225 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546461 Sun, 28 Jun 2009 03:43:04 +0100 2546461 http://www.medworm.com/index.php?rid=2546458&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442226%26dopt%3DAbstract Authors: Hu MY, Lam CT, Liu KD, Xu Z, Fatima S, Su YC, Tsang F, Chen J, Pang JZ, Qin LX, Luk JM A monoclonal antibody, McAb9E (IgG3), was generated against a metastatic HCC cell line, MHCC-1. The antigen was characterized as human Caveolin-1 (Cav-1, 21kDa), with pI of 5.65. The Cav-1 antigen was found significantly over expressed in metastatic HCC cell lines as well as in tumor specimens. The Cav-1 specific McAb may be a useful molecular agent for metastatic HCC. PMID: 19442226 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546458 Sun, 28 Jun 2009 03:43:04 +0100 2546458 http://www.medworm.com/index.php?rid=2546456&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442227%26dopt%3DAbstract Authors: Du H, Huang X, Wang S, Wu Y, Xu W, Li M Proteasome subunit alpha type 7(PSMA7) is an alpha-type subunit of the 20S proteasome core complex and participates in degrading proteins through ubiquitin-proteasome pathway (UPP) which plays an important role in the regulation of cell proliferation or cell cycle control, transcriptional regulation, immune and stress response, cell differentiation, and apoptosis. Previous studies have demonstrated that PSMA7 can be a target interacting with some important proteins involved in transcription factor regulation, cell cycle transition, viral replication and even tumor initiation and progression, suggesting that PSMA7 could be a potential target for the development of clinical diagnosis and new therapeutic drugs. Here, we review the recent st... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546456 Sun, 28 Jun 2009 03:43:04 +0100 2546456 http://www.medworm.com/index.php?rid=2546454&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442228%26dopt%3DAbstract Authors: Guan SP, Mok YK, Koo KN, Chu KL, Wong WS Human chitinases (EC.3.2.1.14) are classified into family 18 of glycosyl hydrolase (GH18) superfamily based on their amino acid sequence similarities. Active chitinase hydrolyzes chitin, a beta-1,4-linked N-acetyl-D-glucosamine oligosaccharide. Chitin is a major structural component of the insect exoskeletons and fungal cell walls, but is not found in vertebrates. In human, eight GH18 chitinases have been identified including active chitotriosidase and acidic mammalian chitinase. Most of the human chitinases lack chitinolytic activity due to mutation of an essential glutamic acid residue at the catalytic domain, and they are termed chitolectin. This review highlights some characteristics of human chitinases, compares structural differen... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546454 Sun, 28 Jun 2009 03:43:04 +0100 2546454 http://www.medworm.com/index.php?rid=2546452&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442229%26dopt%3DAbstract Authors: Kim YS, Yoo HS, Ko JH Aberrant glycosylation is frequently found in cancer, and efforts for biomarker discovery include the preparation of aberrant glycoproteins as promising analytes. Several lectins that bind to aberrant glycans and can be thus used to capture and enrich aberrant glycoproteins in the frontal stage during biomarker discovery are to be introduced. PMID: 19442229 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546452 Sun, 28 Jun 2009 03:43:04 +0100 2546452 http://www.medworm.com/index.php?rid=2546450&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442230%26dopt%3DAbstract Authors: Lu WJ, Lee NP, Fatima S, Luk JM Heat shock proteins (HSPs) consist of a large group of proteins with negligible expressions under physiological conditions. Their expressions are highly induced under stress conditions and they are ubiquitously expressed in various tissues and organs. HSPs possess chaperone functions, thus facilitating the correct folding of proteins or peptides. In hepatocellular carcinoma (HCC), high expressions of HSPs are demonstrated in liver cancer tissues and are correlated clinically with the severity of tumors and poor outcomes of HCC patients. This property enables them to be used as diagnostic markers for the onset of HCC. Since their expressions are highly expressed in liver cancer conditions, inhibitors or antisense oligonucleotides of HSPs are post... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546450 Sun, 28 Jun 2009 03:43:04 +0100 2546450 http://www.medworm.com/index.php?rid=2546448&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442231%26dopt%3DAbstract Authors: Deocaris CC, Kaul SC, Wadhwa R Age- and stress-induced modulations in chaperone systems result in "chaperono-deficiency" or "chaperon-opulence". Development of modulators, of chaperone function has therefore, become an emerging field in drug development and discovery. This mini-review summarizes (i) the events leading to identification of an Hsp70 family stress chaperone, mortalin, (ii) experimental evidence to its role in old age diseases and cancer, and (iii) proposes it as a chaperono-therapeutic agent. As post-translational modifications and expression changes in mortalin are being explored as a biomarker for cancer, cardiovascular diseases and neurodegeneration, we discuss here how the current tools used in studying mortalin (e.g. antibodies, peptides, ribozymes, antisens... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546448 Sun, 28 Jun 2009 03:43:04 +0100 2546448 http://www.medworm.com/index.php?rid=2546446&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442232%26dopt%3DAbstract Authors: Tsang FH, Lee NP, Luk JM Hepatocellular carcinoma (HCC) is a malignant tumor unresponsive to most current therapies. Small peptides, either synthetic or derived from natural proteins, are found promising in treating HCC. Herein, different types of small peptides and their associated mechanistic actions against tumors are discussed, postulating their use as alternative treatments for HCC. PMID: 19442232 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546446 Sun, 28 Jun 2009 03:43:04 +0100 2546446 http://www.medworm.com/index.php?rid=2546444&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442233%26dopt%3DAbstract Authors: Wong KF, Luk JM Bacterial endotoxin [e.g. lipopolysaccharide (LPS)] can trigger systemic hyper-inflammatory that subsequently leads to multiple organ failure and lethality (gram-negative sepsis). This paper describes the development of endotoxin-neutralizing peptides that potentially treat sepsis. These peptides have been derived from bactericidal/permeability-increasing protein (BPIP), anti-microbial peptides, and leukocyte CD18 antigen and some of these peptides have been tested in clinical studies. PMID: 19442233 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546444 Sun, 28 Jun 2009 03:43:04 +0100 2546444 http://www.medworm.com/index.php?rid=2546442&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442234%26dopt%3DAbstract Authors: Carrilho DM, Duarte IC, Francisco R, Ricardo CP, Duque-Magalhães MC Five novel metalloproteinase protein inhibitors (MPIs) with molecular mass between 5.6 and 8.9 kDa and acid/neutral pI were detected in lupin seeds and exhibited strong inhibitory activities against thermolysin and/or gelatinase B. These novel peptides constitute not only the first MPIs described in plants but also the first plant peptides with inhibitory activity against a matrixin. PMID: 19442234 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546442 Sun, 28 Jun 2009 03:43:04 +0100 2546442 http://www.medworm.com/index.php?rid=2546440&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442235%26dopt%3DAbstract Authors: Ding YS, Zhang TL, Gu Q, Zhao PY, Chou KC Prediction of protein secondary structure is somewhat reminiscent of the efforts by many previous investigators but yet still worthy of revisiting it owing to its importance in protein science. Several studies indicate that the knowledge of protein structural classes can provide useful information towards the determination of protein secondary structure. Particularly, the performance of prediction algorithms developed recently have been improved rapidly by incorporating homologous multiple sequences alignment information. Unfortunately, this kind of information is not available for a significant amount of proteins. In view of this, it is necessary to develop the method based on the query protein sequence alone, the so-called single-seq... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546440 Sun, 28 Jun 2009 03:43:04 +0100 2546440 http://www.medworm.com/index.php?rid=2546438&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19442236%26dopt%3DAbstract Authors: Zhi-Hua L, Huai-Liang W, Bo Z, Yuan-Qiang W, Yong L, Yu-Zhang W A set of 70 peptides with affinity for the class I MHC HLA-A*0201 molecule was subjected to quantitative analyses of structure-affinity relationship based on the SCORE function with good results (r(2)=0.6982, q(2)=0.6188, RMS=0.280). Then the 'leave-one-out' cross-validation (LOO-CV) and an outer test set including 18 outer samples were used to validate the QSAR model, and the results show that the QSAR model has good predictability for outside samples. Statistical analysis showed that the hydrophobic and hydrogen bond interaction played a significant role in peptide-MHC molecule binding. The study also provided useful information for structure modification of CTL epitope, and laid theoretical base for molecular d... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546438 Sun, 28 Jun 2009 03:43:04 +0100 2546438 http://www.medworm.com/index.php?rid=2546369&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519513%26dopt%3DAbstract Authors: Tutar Y PMID: 19519513 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546369 Sun, 28 Jun 2009 03:43:04 +0100 2546369 http://www.medworm.com/index.php?rid=2546368&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519514%26dopt%3DAbstract Authors: Sharma D, Masison DC Heat shock proteins protect cells from various conditions of stress. Hsp70, the most ubiquitous and highly conserved Hsp, helps proteins adopt native conformation or regain function after misfolding. Various co-chaperones specify Hsp70 function and broaden its substrate range. We discuss Hsp70 structure and function, regulation by co-factors and influence on propagation of yeast prions. PMID: 19519514 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546368 Sun, 28 Jun 2009 03:43:04 +0100 2546368 http://www.medworm.com/index.php?rid=2546367&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519515%26dopt%3DAbstract Authors: Guinan E, Jones GW Chaperones have long been recognised for their essential roles in the cell. They are involved in the refolding or degradation of misfolded proteins as well as the correct folding of newly synthesised proteins. However recent experiments have discovered that chaperones also have an important role to play in the propagation and maintenance of prions in yeast. The following minireview focuses on the Hsp70 chaperone family and it's involvement in the propagation of yeast prions. PMID: 19519515 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546367 Sun, 28 Jun 2009 03:43:04 +0100 2546367 http://www.medworm.com/index.php?rid=2546366&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519516%26dopt%3DAbstract Authors: Glover JR, Lum R Hsp104 is molecular chaperone in the AAA+ family of ATPases that specializes in the resolubilization and refolding of thermally denatured proteins in yeast. In addition to providing high levels of thermotolerance, Hsp104 plays a pivotal role in the propagation of yeast prions, self-replicating, amyloid-like aggregates that are inherited during mitosis and meiosis. In this review, the structure and function of Hsp104 is discussed, its functional interaction with other molecular chaperones, and a model for disaggregation and refolding is proposed. PMID: 19519516 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546366 Sun, 28 Jun 2009 03:43:04 +0100 2546366 http://www.medworm.com/index.php?rid=2546365&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519517%26dopt%3DAbstract Authors: Romanova NV, Chernoff YO High-ordered aggregates (amyloids) may disrupt cell functions, cause toxicity at certain conditions and provide a basis for self-perpetuated, protein-based infectious heritable agents (prions). Heat shock proteins acting as molecular chaperones counteract protein aggregation and influence amyloid propagation. The yeast Hsp104/Hsp70/Hsp40 chaperone complex plays a crucial role in interactions with both ordered and unordered aggregates. The main focus of this review will be on the Hsp104 chaperone, a molecular "disaggregase". PMID: 19519517 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546365 Sun, 28 Jun 2009 03:43:04 +0100 2546365 http://www.medworm.com/index.php?rid=2546364&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519518%26dopt%3DAbstract Authors: Li J, Qian X, Sha B The mechanism by which Hsp40 and other molecular chaperones recognize and interact with non-native polypeptides is a fundamental question, as is how Hsp40 co-operates with Hsp70 to facilitate protein folding. Years of structural studies of Hsp40 from yeast and other species, conducted using X-ray protein crystallography, NMR and small-angle X-ray scattering, have shed light on the mechanisms how Hsp40 functions as a molecular chaperone and how Hsp40-Hsp70 pair promotes protein folding, protein transport and degradation. This review provides a discussion of recent structural studies of Hsp40s and their functional implications. PMID: 19519518 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546364 Sun, 28 Jun 2009 03:43:04 +0100 2546364 http://www.medworm.com/index.php?rid=2546363&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519519%26dopt%3DAbstract Authors: Kocabiyik S Small heat shock proteins are ubiquitously found in all three domains of life, although they are the most poorly conserved family of molecular chaperones. Their involvement in anti-stress mechanisms of the cells have been clearly demonstrated by induction of their expression in response to various environmental and pathological stresses. Small heat shock proteins comprise the most effective chaperone family concerning their unusual capacity of substrate binding. It is well documented that small heat shock proteins associate with unfolding substrate proteins and form large oligomeric complexes to prevent their aggregation and accumulation, that otherwise would impair the normal cell functions. The substrates captured by small heat shock proteins are further refolded... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546363 Sun, 28 Jun 2009 03:43:04 +0100 2546363 http://www.medworm.com/index.php?rid=2546362&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519520%26dopt%3DAbstract Authors: Kabani M Since their recent identification, eukaryotic Hsp70 nucleotide exchange factors (NEFs) have gained increasing interest due to their engagement in vital cellular processes. Here, I summarize our current knowledge of their mechanisms of action, regulations and cellular functions as well as their relevance for human diseases such as cystic fibrosis or amyloidoses. PMID: 19519520 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546362 Sun, 28 Jun 2009 03:43:04 +0100 2546362 http://www.medworm.com/index.php?rid=2546361&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519521%26dopt%3DAbstract This article focuses on ribosome-associated chaperones. A chaperone bound close to the exit tunnel on a ribosome 25 A from the emerging nascent chain has an effective concentration of 1 x 10(-1) M, which is 4-5 orders of magnitude larger than the concentration of the chaperone in the cytosol. Ribosome-bound chaperones bind nascent chains intramolecularly with rates as large as 10(4) s(-1) in order to keep chains unfolded. PMID: 19519521 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546361 Sun, 28 Jun 2009 03:43:04 +0100 2546361 http://www.medworm.com/index.php?rid=2546360&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519522%26dopt%3DAbstract Authors: Greene LE, Park YN, Masison DC, Eisenberg E Fluorescent live cell imaging has recently been used in numerous studies to examine prions in yeast. These fluorescence studies take advantage of the fact that unlike the normally folded form, the misfolded amyloid form of the prion protein is aggregated. The studies have used fluorescence to identify new prions, to study the transmission of prion from mother to daughter, and to understand the role of molecular chaperones in this transmission. The use of fluorescence imaging complements the more standard methods used to study prion propagation. This review discusses the various studies that have taken advantage of fluorescence imaging technique particularly in regard to understanding the transmission and curing of the [PSI(+)], the p... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546360 Sun, 28 Jun 2009 03:43:04 +0100 2546360 http://www.medworm.com/index.php?rid=2546359&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519523%26dopt%3DAbstract Authors: Lee HC, Zhang L The Hsp90 and Hsp70 molecular chaperones play important roles in the folding and proper functioning of diverse cellular proteins, including transcriptional regulators and protein kinases. In yeast, several transcriptional regulators and protein kinases are known to be substrates for Hsp90 and Hsp70 molecular chaperones. The yeast heme activator protein Hap1 promotes transcription of many genes in response to heme. It requires Hsp90 and Hsp70 molecular chaperones for its activity to be precisely regulated by heme concentration. The mechanism by which molecular chaperones promote heme regulation of Hap1 activity is distinct from the mechanism by which molecular chaperones promote steroid signaling. Hsp70 and Hsp90 molecular chaperones act separately to promote Ha... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546359 Sun, 28 Jun 2009 03:43:04 +0100 2546359 http://www.medworm.com/index.php?rid=2546358&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519524%26dopt%3DAbstract Authors: de Farias CB, Stertz L, Lima RC, Kapczinski F, Schwartsmann G, Roesler R The gastrin-releasing peptide receptor (GRPR) is a therapeutic target in colon cancer. Here we show that the GRPR antagonist RC-3095 (10(-3), 10(-6), or 1 microM) decreases nerve growth factor (NGF) secretion measured by enzyme-linked immunosorbent assay (ELISA) in HT-29 human colon carcinoma cells. The results suggest that decreased secretion of neurotrophins might be a novel mechanism by which GRPR antagonists exert their antiproliferative effects in cancer cells. PMID: 19519524 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546358 Sun, 28 Jun 2009 03:43:04 +0100 2546358 http://www.medworm.com/index.php?rid=2546357&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519525%26dopt%3DAbstract Authors: Sharifi E, Sattarahmady N, Habibi-Rezaei M, Farhadi M, Sheibani N, Ahmad F, Moosavi-Movahedi AA The effects of beta-cyclodextrin (beta-CyD) and trehalose on glycation of human serum albumin (HSA) were studied. These additives reduced AGEs and nanofibril formation of HSA under in vitro glycation conditions and improved its helical structure. These were accomplished through direct interactions of them with HSA and alterations in solute-protein interactions. PMID: 19519525 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546357 Sun, 28 Jun 2009 03:43:04 +0100 2546357 http://www.medworm.com/index.php?rid=2546356&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519526%26dopt%3DAbstract Authors: Hasani L, Ranjbar B, Tavallaie M, Sadeghizadeh M C-terminal fragment of the Botulinum neurotoxin A comprises two sub-domains including H(C)-N and H(C)-C. Here, the conformational change of H(C)-N was studied by spectroscopic techniques. The results indicated that the partially unfolded state forms during unfolding of H(C)-N. This finding may shed light on poorly--known features of the protein. PMID: 19519526 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546356 Sun, 28 Jun 2009 03:43:04 +0100 2546356 http://www.medworm.com/index.php?rid=2546355&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519527%26dopt%3DAbstract Authors: Jeon E, Jang JH The engineering of a novel FGF2 fused with highly conserved bone mineral-binding domain of osteocalcin (OC) for targeting to bone mineral hydroxyapatite (HA) exhibited much stronger HA-binding affinity than native FGF2. FGF2-OC also showed a significant increase of mitogenic activity and cellular differentiation of osteoblastic cells compared with native FGF2. PMID: 19519527 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546355 Sun, 28 Jun 2009 03:43:04 +0100 2546355 http://www.medworm.com/index.php?rid=2546354&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519528%26dopt%3DAbstract We describe a quick and reliable method for the production of HBD2 in Escherichia coli. HBD2 was expressed as an insoluble fusion, chemically cleaved and oxidised to give a single, folded HBD2 beta-isoform. The purified peptide was analysed by high resolution mass spectrometry, displayed a well-dispersed (1)H NMR spectrum, was a chemoattractant to HEK293 cells expressing CCR6 and acted as an antimicrobial agent against E. coli, P. aeruginosa, C. albicans and S. aureus. PMID: 19519528 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546354 Sun, 28 Jun 2009 03:43:04 +0100 2546354 http://www.medworm.com/index.php?rid=2546353&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519529%26dopt%3DAbstract Authors: Kawsar SM, Matsumoto R, Fujii Y, Yasumitsu H, Uchiyama H, Hosono M, Nitta K, Hamako J, Matsui T, Kojima N, Ozeki Y The glycan-binding profile of a beta-galactoside-binding 15 kDa lectin (Galectin-1) purified from the oocytes of the American bullfrog, Rana catesbeiana, was studied using 61 pyridyl-aminated oligosaccharides by frontal affinity chromatography. Human blood type-A-hexasaccharide (GalNAcalpha1-3(Fucalpha1-2)Galbeta;1-4GlcNAcbeta1-4Galbeta1-4Glc) was found to exhibit the strongest ligand binding to the galectin while Forssman antigen (GalNAcalpha1-3GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc) and type-A-tetrasaccharide (GalNAcalpha1-3(Fucalpha1-2)Galbeta1-4GlcNAcbeta1-4Glc) were also extensively recognized. The kinetics of affinity of galectin-1 to type-A oligosaccharide w... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546353 Sun, 28 Jun 2009 03:43:04 +0100 2546353 http://www.medworm.com/index.php?rid=2546352&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519530%26dopt%3DAbstract Authors: Hashimoto M, Toorchi M, Matsushita K, Iwasaki Y, Komatsu S To investigate the function of plant plasma membrane, proteins of rice plasma membrane were analyzed and the proteins changed by cold stress were identified. Plasma membrane proteins were purified with an aqueous two-phase partitioning method from root of rice seedlings, and activity of specific H(+)-ATPase localized in plasma membranes was measured. The plasma membrane proteins were separated by SDS-PAGE or 2D-PAGE, and analyzed with nano LC-MS/MS. The number of transmembrane helices was predicted from the amino acid sequence of annotated proteins. Functional categorization revealed that the most of proteins were associated with energy production, signal transduction, protein synthesis, cell growth/division and defens... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546352 Sun, 28 Jun 2009 03:43:04 +0100 2546352 http://www.medworm.com/index.php?rid=2546351&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519531%26dopt%3DAbstract Authors: Deng XY, Li WR, Sun YW, Wei HD, Jiang Y, He FC To further clarify the priming mechanism of liver regeneration, proteins and protein complexes from rat plasma (normal group, partial hepatectomy (PHx) group and sham-operation group) were comparatively studied by two-dimensional gel electrophoresis and two-dimensional blue native gel electrophoresis. Our results suggested that Kupffer cell--NF-kappaB/ROS might trigger the liver regeneration. PMID: 19519531 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546351 Sun, 28 Jun 2009 03:43:04 +0100 2546351 http://www.medworm.com/index.php?rid=2546350&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519532%26dopt%3DAbstract In this study, we investigated the potential use of Tat signal peptide from S. coelicolor to improve secretory expression. The results showed that Tat signal peptide (ssDagA) could effectively secrete active Green fluorescent protein (GFP) to periplasm. When the rare codons of signal sequence were optimized, the expression and secretion yield of GFP improved by about 2-3 folds as detected qualitatively by western blotting and fluorescent analysis. The increase of translation rate could be explained by the unstability of mRNA secondary structure. In summary, our strategy could provide a new approach for high-level secretory expression of heterologous proteins in E. coli. PMID: 19519532 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2546350 Sun, 28 Jun 2009 03:43:04 +0100 2546350 http://www.medworm.com/index.php?rid=2323955&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356129%26dopt%3DAbstract Authors: Slusarz MJ, Slusarz R, Ciarkowski J The role of the internal water molecules in vasopressin and oxytocin receptors has been investigated via molecular dynamics simulations in hydrated membrane model. Several water molecules have been identified within the binding pockets of receptors, where they interact with the conserved residues. In all unliganded receptors, the water molecules bound to the highly conserved D2.50 cluster have been observed. It has been proposed which water molecules may significantly contribute to the stability of overall receptor structure. In receptor-ligand complexes the water molecules are involved in the receptor-ligand interactions by forming water-mediated hydrogen bonds at their contact surface. PMID: 19356129 [PubMed - in process] (Source: Prot... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323955 Sat, 11 Apr 2009 17:41:47 +0100 2323955 http://www.medworm.com/index.php?rid=2323952&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356130%26dopt%3DAbstract Authors: Ding H, Luo L, Lin H Discriminating cell wall lytic enzymes from non lytic enzymes is a very important task for curing bacterial infections. In this paper, based on Chou's amphiphilic pseudo amino acid composition, we develop fisher-discriminant based classifier to predict cell wall lytic enzymes. Experiments show that 66.7% sensitivity with 88.6% specificity is obtained. The method is further able to predict endolysin and autolysin with an overall accuracy of 92.9%. Results demonstrated that our method can provide highly useful information for further bacterial control research. PMID: 19356130 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323952 Sat, 11 Apr 2009 17:41:47 +0100 2323952 http://www.medworm.com/index.php?rid=2323949&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356131%26dopt%3DAbstract Authors: Ghaffar A, Khan SA, Mukhtar Z, Latif F, Rajoka MI The xylanase (Xyn11A) gene (883 bp) was amplified using C. thermophilum DNA as template and cloned into pET-32a (+) and expressed in E. coli BL21 under T(7) promoter. The recombinant xylanase on SDS-PAGE had a molecular mass of 30 kDa. Productivity profiles of xylanase in E. coli recombinant are more than 4-fold of that produced from T. reesei RUTC-30, 5-fold of that produced by the donor and significantly higher than the values reported on other E. coli, and Saccharomyces cerevisiae recombinants. Temperature stability, pH stability, and other kinetic parameters confirmed that the gene product was thermo-stable in alkaline buffer favoring its suitability to bio-bleaching of kraft pulp. PMID: 19356131 [PubMed - in process] (... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323949 Sat, 11 Apr 2009 17:41:47 +0100 2323949 http://www.medworm.com/index.php?rid=2323946&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356132%26dopt%3DAbstract Authors: Hianik T, Porfireva A, Grman I, Evtugyn G Novel affinity biosensors for detecting cellular prions, PrP(C), based on DNA aptamers and antibodies immobilized onto the carbon nanotubes have been designed and compared in accordance with their binding ability and analytical performance. The biosensors allowed us to detect PrP(C) with the limits of detection of 20 to 50 pM. PMID: 19356132 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323946 Sat, 11 Apr 2009 17:41:47 +0100 2323946 http://www.medworm.com/index.php?rid=2323943&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356133%26dopt%3DAbstract Authors: Man N, Yu L, Zheng F, Li Y, Wen LP We synthesized a 15-amino acid bi-functional synthetic peptide, RPC2, with the sequence Ac-CGKRKWSQ PKKKRKV-Cysteamide, which consists of a 7-amino acid nuclear localization signal (NLS) domain at the carboxyl terminus that electrostatically binds DNA and a 5-amino-acid tumor-homing domain at the amino terminus. This peptide efficiently delivered GFP and Renilla luciferase reporter genes into rat primary osteoblastic cells while exhibiting low cytotoxicity. The optimal delivery was achieved when the ratio of DNA: RPC2 reached 1:10 (w/w). Transfection efficiency can be further enhanced by the addition of Lipofectamine 2000 and modification of RPC2. These results indicated that RPC2 can deliver exogenous DNA into primary osteoblastic cells with... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323943 Sat, 11 Apr 2009 17:41:47 +0100 2323943 http://www.medworm.com/index.php?rid=2323940&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356134%26dopt%3DAbstract Authors: Chen Y, Han K Hepatitis C virus (HCV) infection is a major cause of liver disease and a dangerous threat to public health. Hence, the problem of finding interactions between HCV and human proteins has received much attention. In this paper, we present an approach to predicting binding residues in HCV proteins using a support vector machine (SVM) classifier. Based on six biochemical properties of amino acids (sequence profile, accessible surface area, residue binding propensity, sequence entropy, hydrophobicity and conservation weight), the SVM classifier achieved an average accuracy of 93%. Contiguous residues in the sequence act together to determine a binding site, and a window of 11 residues (the target residue and 5 adjacent residues on each side) gave the best result in o... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323940 Sat, 11 Apr 2009 17:41:47 +0100 2323940 http://www.medworm.com/index.php?rid=2323937&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356135%26dopt%3DAbstract Authors: Aparoy P, Chatterjee M, Guruprasad L, Reddanna P Prohormone or proprotein convertases (PC2) are members of the subtilisin family of serine proteases. They are involved in the activation of precursor molecules by endoproteolytic cleavage at basic amino acid residues within the general motif (K/R)-(X)n- (K/R)2, where n is 0, 2, 4 or 6 and X is usually not Cys. Among the members of this prohormone convertase family, Neuroendocrine Convertase-2 (NEC-2) is regarded as one of the important proteins involved in the maturation of many precursor proteins. Being widely distributed in the neuroendocrine cells, these proteins play a vital role in causing malignant gliomas. They can serve as important drug targets in the treatment of cancers. In the present study, a 3D model of NEC-2 was g... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323937 Sat, 11 Apr 2009 17:41:47 +0100 2323937 http://www.medworm.com/index.php?rid=2323935&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356136%26dopt%3DAbstract Authors: Bayryamov SG, Vassilev NG, Rangelov MA, Mladjova AP, Petkov DD 2'/3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-Ado (1) and its deoxy analog: 3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-2'-dAdo (2) were designed and synthesized as substrates for the model ribosome reaction we used to demonstrate the crucial role of A76 2'-OH of peptidyl-tRNA in the rate acceleration of peptide bond formation during protein biosynthesis. PMID: 19356136 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323935 Sat, 11 Apr 2009 17:41:47 +0100 2323935 http://www.medworm.com/index.php?rid=2323932&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356137%26dopt%3DAbstract Authors: Longshaw VM, Stephens LL, Daniel S, Blatch GL The role of the TPR2B domain of Hop is as yet unknown. We have shown here by site directed mutagenesis and size exclusion chromatography for the first time that the TPR1 and TPR2B domains of Hop independently dimerized, and that the dimerization of TPR2B was not dependent on its predicted two-carboxylate clamp residues. Furthermore, our data indicated that the dimerization of Hop and its domains was not disrupted in the presence of Hsp70 and Hsp90 peptides. PMID: 19356137 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323932 Sat, 11 Apr 2009 17:41:47 +0100 2323932 http://www.medworm.com/index.php?rid=2323929&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356138%26dopt%3DAbstract Authors: Lesner A, Wysocka M, Solek M, Legowska A, Rolka K A series of aldehyde inhibitors with the general formula Ac-Phe-Val-Thr-X-CHO, where X = Lys, Arg, Phe, Tyr, p-nitro-L-phenylalanine (Nif), p-amino-L-phenylalanine (Amf), p-guanidine-L-phenylalanine (Gnf), pyridyl-L-alanine (Pal), was synthesized. The starting structure of this series based on our previous work on cathepsin G chromogenic substrates. The synthesis of all compounds was performed in solid phase applying Fmoc chemistry. We investigated the inhibitory potency of the obtained compounds against cathepsin G and bovine alpha-chymotrypsin and evaluated their dissociation constants (K(i)). The studied peptides displayed different inhibition profiles and potency. As a result, a potent and selective inhibitor of cathepsin G... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323929 Sat, 11 Apr 2009 17:41:47 +0100 2323929 http://www.medworm.com/index.php?rid=2323927&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356139%26dopt%3DAbstract Authors: Hisamatsu K, Unno H, Goda S, Hatakeyama T The hemolytic lectin CEL-III and its site-directed mutants were expressed in Escherichia coli cells. Replacement of the valine clusters in domain 3 with alanine residues led to increased self-oligomerization in solution and higher hemolytic activity. The results suggest the involvement of these valine clusters in CEL-III oligomerization and hemolytic activity. PMID: 19356139 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323927 Sat, 11 Apr 2009 17:41:47 +0100 2323927 http://www.medworm.com/index.php?rid=2323925&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356140%26dopt%3DAbstract Authors: Kumar A, Reddy S, Srinivasan N, Nandi D The role of interaction between Asn259 (catalytic domain) with Gln821 (C-terminal domain) in PeptidaseN was investigated. The k(cat) of PeptidaseN containing Asn259Asp or Gln821Glu is enhanced whereas it is suppressed in Asn259AspGln821Glu. Structural analysis shows this interaction to change the relative disposition of active site residues, which modulates catalytic activity. PMID: 19356140 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323925 Sat, 11 Apr 2009 17:41:47 +0100 2323925 http://www.medworm.com/index.php?rid=2323923&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356141%26dopt%3DAbstract Authors: Fatima S, Khan RH The equilibrium denaturation pathway of Succinyl Con A exhibited three-state mechanism with the transition midpoints at 1 and 3 M GdnHCl and at 2.6 and 5 M urea. Unfolding resulted in stabilization of molten-globule (MG) like intermediate states at 2 M GdnHCl and 3 M urea. It was particularly interesting that state obtained at 3 M urea was functionally active. PMID: 19356141 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323923 Sat, 11 Apr 2009 17:41:47 +0100 2323923 http://www.medworm.com/index.php?rid=2323921&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356142%26dopt%3DAbstract Authors: Padovan L, Segat L, Tossi A, Antcheva N, Benko-Iseppon AM, Ederson AK, Brandao L, Calsa T, Crovella S Comparing available Poaceae defensins with sugarcane ESTs, a putative defensin gene was identified in sugarcane and cloned from genomic sugarcane DNA. The deduced encoded peptide shows the structure and amino acid composition typical of other plant defensins. Using RT-PCR, defensin expression in sugarcane and differences between "normal" and infected sugarcane were evidenced. PMID: 19356142 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323921 Sat, 11 Apr 2009 17:41:47 +0100 2323921 http://www.medworm.com/index.php?rid=2323919&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356143%26dopt%3DAbstract Authors: Sukumari-Ramesh S, Lemosy EK The Drosophila proteases Gastrulation Defective and Snake function in embryonic polarity establishment and bind heparin, a surrogate for anionic species present in the extracellular matrix. Here we demonstrate binding of GD, but not Snake, to anionic species that appear to be tightly associated with a highly purified eggshell matrix. PMID: 19356143 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323919 Sat, 11 Apr 2009 17:41:47 +0100 2323919 http://www.medworm.com/index.php?rid=2323917&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356144%26dopt%3DAbstract Authors: Jaenicke E, Pairet B Hemoglobin is the versatile oxygen carrier in the blood of vertebrates and a key factor for adaptation to live in high altitudes. Several structural changes are known to account for increased oxygen affinity in hemoglobin of altitude adapted animals such as llama and barheaded goose. Guinea pigs are adapted to live in high altitudes in the Andes and consequently their hemoglobin has an increased oxygen affinity. However, the structural changes responsible for the adaptation of guinea pig hemoglobin are unknown. Here we report the crystallization of guinea pig hemoglobin in the presence of 2.6 M ammonium sulfate and a preliminary analysis of the crystals. Crystals diffract up to a resolution of 2.0 A. They are orthorhombic with space group C 2 2 2(1) and ce... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323917 Sat, 11 Apr 2009 17:41:47 +0100 2323917 http://www.medworm.com/index.php?rid=2323915&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356145%26dopt%3DAbstract Authors: Shiroishi M, Maenaka K Human leukocyte antigen-G (HLA-G) is a nonclassical MHC class I (MHCI) molecule that is expressed mainly on placenta trophoblast cells. Leukocyte Ig-like receptor B2 (LILRB2) is a human inhibitory immune receptor that recognizes HLA-G with a higher affinity than any other MHCI although this interaction is only in the microM range. The interaction between HLA-G and LILRB2 seems to play a dominant role in the escape of the fetus from the maternal immune response. Here we report the crystallization and x-ray analysis of the LILRB2/HLA-G complex. The extracellular domains of HLA-G and LILRB2 were expressed in Escherichia coli, refolded and purified. The initial crystallization trials using novel PEG-based screening sets provided crystals of the LILRB2/HLA-G ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323915 Sat, 11 Apr 2009 17:41:47 +0100 2323915 http://www.medworm.com/index.php?rid=2323913&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356146%26dopt%3DAbstract Authors: Chen H, Huang H, Li X, Tong S, Niu L, Teng M Saccharomyces cerevisae ARO9 protein, an aromatic aminotransferase II, catalyzes the transamination step of the catabolism of aromatic amino acids, mainly tryptophan. ARO9 also belongs to a novel subfamily of enzymes within the aminotransferase subgroup I. Crystals of ARO9 protein have been grown using the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 75.6 A, b = 117.5 A, c = 134.9 A. Diffraction data were collected to a resolution of 2.6 A using a rotating-anode X-ray source. Analysis indicates the presence of two molecules in an asymmetric unit. PMID: 19356146 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323913 Sat, 11 Apr 2009 17:41:47 +0100 2323913 http://www.medworm.com/index.php?rid=2323911&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356147%26dopt%3DAbstract Authors: Moorthy PS, Neelagandan K, Balasubramanian M, Ponnuswamy MN Hemoglobin is a vital protein present in almost all higher species. It is a transport protein involved in carrying oxygen from lungs to tissues and carbon dioxide back to lungs by an intrinsically coordinated manner. Even though a good amount of work has been carried out in this direction there exists scarcity of structural insight on low oxygen affinity species. Attempts are being made to unravel the structural insight of this low oxygen affinity species. Goat blood plasma was collected, treated with EDTA to avoid blood clotting and purification was accomplished using DEAE-anion chromatographic column. The goat hemoglobin was crystallized using 50mM of phosphate buffer at pH 6.7 with 1M NaCl and PEG 3350 as precipita... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2323911 Sat, 11 Apr 2009 17:41:47 +0100 2323911 http://www.medworm.com/index.php?rid=2257642&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275733%26dopt%3DAbstract Authors: Sakudo A PMID: 19275733 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257642 Fri, 13 Mar 2009 03:33:06 +0100 2257642 http://www.medworm.com/index.php?rid=2257641&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275734%26dopt%3DAbstract Authors: Sakudo A, Ikuta K Prion diseases are fatal degenerative disorders whose features include the accumulation of abnormal isoform of prion protein (PrP(Sc)), vacuolation, and astrocytosis in the brain. After a prion infection, the cellular isoform of prion protein (PrP(C)) is converted into PrP(Sc), resulting in PrP(C) deficiency and PrP(Sc) accumulation in the brain. These changes are major etiological events, thought to be closely related to the pathogenesis of prion diseases, and used as an index for diagnosis. Studies using recently developed research tools such as transgenic and knockout mice and cell lines have shown that the accumulation of PrP(Sc) is not the sole factor contributing to the clinical onset of prion diseases and that loss-of function of PrP(C) by depletion le... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257641 Fri, 13 Mar 2009 03:33:06 +0100 2257641 http://www.medworm.com/index.php?rid=2257640&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275735%26dopt%3DAbstract Authors: Vassallo N Prion diseases are neurodegenerative disorders characterized by a hallmark event involving the post-translational misfolding of the normal cellular prion protein (PrP(C)) into an infectious and toxic protease-resistant conformation (PrP(Sc)). Studies on identification of the pathological prion species and on the mechanisms involved in triggering neuronal death have been hampered by the heterogeneous nature of PrP(Sc) aggregates. The use of synthetic PrP-derived peptides has made possible exploration of the relationship between amino acid sequence, biophysical structure and biological effect. Indeed, most PrP-derived peptides replicate the fundamental aspects of full-length PrP(Sc), including: a beta-sheet-rich structure; destabilization of lipid membranes; intracell... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257640 Fri, 13 Mar 2009 03:33:06 +0100 2257640 http://www.medworm.com/index.php?rid=2257639&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275736%26dopt%3DAbstract Authors: Nitta K, Sakudo A, Masuyama J, Xue G, Sugiura K, Onodera T The cellular isoform of prion proteins (PrP(C)) is expressed in hematopoietic stem cells, granulocytes, T and B lymphocyte natural killer cells, platelets, monocytes, dendritic cells, and follicular dendritic cells, which may act as carrier cells for the spread of its abnormal isoform (PrP(Sc)) before manifesting transmissible spongiform encephalopathies (TSEs). In particular, macrophages and dendritic cells seem to be involved in the replication of PrP(Sc) after ingestion. In addition, information on the role of PrP(C) during phagocytotic activity in these cells has been obtained. A recent study showed that resident macrophages from ZrchI PrP gene (Prnp)-deficient (Prnp(-/-)) mice show augmented phagocytotic activity ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257639 Fri, 13 Mar 2009 03:33:06 +0100 2257639 http://www.medworm.com/index.php?rid=2257638&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275737%26dopt%3DAbstract Authors: Ano Y, Sakudo A, Nakayama H, Onodera T Transmissible spongiform encephalopathies (TSEs) are characterized by the accumulation of a protease-resistant abnormal isoform of the prion protein (PrP(Sc)), which is converted from the cellular isoform of the prion protein (PrP(C)). In the oral transmission of prion protein, PrP(Sc) can invade a host body through the intestinal tract. There is only limited information available on how the infectious agent passes through one or several biological barriers before it can finally reach the brain. After oral administration, PrP(Sc) withstands the digestive process and may be incorporated by microfold (M) cells or villous columnar epithelial cells in the intestine. After entry into the intestinal epithelium, PrP(Sc) accumulates and is amplif... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257638 Fri, 13 Mar 2009 03:33:06 +0100 2257638 http://www.medworm.com/index.php?rid=2257637&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275738%26dopt%3DAbstract Authors: Atarashi R The development of amplification technology for abnormal forms of prion protein in vitro has had a great impact on the field of prion research. This novel technology has generated new possibilities for understanding the molecular basis of prions and for developing an early diagnostic test for prion diseases. This review provides an overview of recent progress in cell-free PrP(Sc) amplification techniques. PMID: 19275738 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257637 Fri, 13 Mar 2009 03:33:06 +0100 2257637 http://www.medworm.com/index.php?rid=2257636&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275739%26dopt%3DAbstract Authors: Sakaguchi S Emergence of variant type of Creutzfeldt-Jakob disease (vCJD) in humans due to infection from bovine spongiform encephalopathy contaminated beef and recent reports of human-to-human transmission of vCJD via blood transfusion have raised great concern about an epidemic of vCJD. The disease is currently difficult to diagnose during pre-clinical stages and requires a very long incubation period for neurological symptoms to be evident. This therefore suggests that the disease is already latently spreading and that opportunity for infection is thus growing among human populations. Interestingly, passive immunization with antibodies against prion protein (PrP), a major component of the prion infectious agents, was shown to protect mice from infection, indicating the poss... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257636 Fri, 13 Mar 2009 03:33:06 +0100 2257636 http://www.medworm.com/index.php?rid=2257635&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275740%26dopt%3DAbstract Authors: Inoue Y Currently, prion phenomena have been detected in various organisms, in addition to mammals affected by transmissible spongiform encephalopathies. In the budding yeast Saccharomyces cerevisiae, various proteins have prion properties and adopt atypical phenotypes as genetic elements, such as the Sup35 and Ure2 proteins, corresponding to the [PSI(+)] and [URE3] phenotypes, respectively. Each yeast prion protein has a prion-forming region rich in glutamines and/or asparagines, and can form amyloid fibrils in its prion conformation. Studies on yeast prions have revealed that the amyloid fibrils play critical roles in the life cycle of the yeast prion. First, the amyloid fibril binds the normal prion protein and catalyzes a structural conversion into the abnormal form, the k... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257635 Fri, 13 Mar 2009 03:33:06 +0100 2257635 http://www.medworm.com/index.php?rid=2257634&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275741%26dopt%3DAbstract Authors: Cheung AH, Wong JH, Ng TB Three trypsin-chymotrypsin inhibitors were isolated from seeds of the black gram (Vigna mungo) with a procedure that entailed cation exchange chromatography on SP-Sepharose, anion exchange chromatography on Q-Sepharose, ion exchange chromatography by fast protein liquid chromatography (FPLC) on Mono Q and Mono S, and gel filtration by FPLC on Superdex 75. Two of the trypsin-chymotrypsin inhibitors were adsorbed on the first four types of chromatographic media. All three inhibitors have a molecular mass of 16 kDa as judged by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The trypsin inhibitory activity of the inhibitors was attenuated in the presence of the reducing agent dithiothreitol. The remaining inhibitor was unads... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257634 Fri, 13 Mar 2009 03:33:06 +0100 2257634 http://www.medworm.com/index.php?rid=2257633&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275742%26dopt%3DAbstract Authors: Nishimaru T, Yamaguchi Y, Wakamiya T NPTX-594 is a neurotoxic acylpolyamine isolated from a Madagascar Joro spider and acts as a specific blocker of glutamate receptors (GluRs). The present study reports the creation of novel NPTX-594 analogs with thiol-containing fluorophores for use as visualization probes for the analysis of the binding mode between spider toxins and GluRs, together with the result of their cricket bioassay. PMID: 19275742 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257633 Fri, 13 Mar 2009 03:33:06 +0100 2257633 http://www.medworm.com/index.php?rid=2257632&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275743%26dopt%3DAbstract In this study, we apply the amino-acid pair predictability to quantifying the human androgen receptor with its 215 missense point mutations to analyze which amino-acid pairs are sensitive to mutations. The results show that 94.88% mutations occurred at the unpredictable amino-acid pairs, 79% mutations targeted at one or two original amino-acid pairs whose actual frequency is larger than predicted frequency and 63.26% mutations lead to one or two mutated amino-acid pairs with their actual frequency smaller than predicted one. PMID: 19275743 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257632 Fri, 13 Mar 2009 03:33:06 +0100 2257632 http://www.medworm.com/index.php?rid=2257631&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275744%26dopt%3DAbstract Authors: Miyazawa T, Ozawa A, Furuhashi M, Munegumi T Stereochemical preference for homochiral or heterochiral couplings was investigated in the reactions of N-protected L-amino acid 1-hydroxybenzotriazole esters with racemic amino acid derivatives. It was found to be dependent on the combination of amino acid residues as the carboxyl and amino components and the protecting groups of the amino acid residues, especially the N-protecting groups. Very high diastereomeric ratios were observed when t-leucine was employed as the carboxyl component and/or proline as the amino component and when the N-protecting group was the phthaloyl group. PMID: 19275744 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257631 Fri, 13 Mar 2009 03:33:06 +0100 2257631 http://www.medworm.com/index.php?rid=2257630&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275745%26dopt%3DAbstract Authors: Zahed M, Suzuki T, Suganami A, Sugiyama H, Harada K, Takiguchi M, Tamura Y, Suzuki N We screened SMG7-binding peptides with phage display and docking simulation analysis. Although a consensus motif was absent in the phage display-derived candidates, we succeeded to find a peptide CDDRPPKSC, which can bind specifically to SMG7. We conclude that docking simulation helps to find high-affinity peptides efficiently, even if the phage display-screened candidates lack a consensus region. PMID: 19275745 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257630 Fri, 13 Mar 2009 03:33:06 +0100 2257630 http://www.medworm.com/index.php?rid=2257629&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275746%26dopt%3DAbstract Authors: Li P, Zhou JY, Zhou YY, Qian CD, Li O, Min H, Wu XC The coiled-coil neck domain of pulmonary surfactant protein D (SP-D) is required for trimeric association and the subsequent assembly of functional dodecamers of SP-D. It is also necessary and sufficient for trimerization of a heterologous collagen sequence. To investigate whether it is capable of driving trimerization of heterologous non-collagenous proteins, we expressed and purified a fusion of a heterologous non-collagenous sequence (thioredoxin) to the coiled-coil neck domain of human SP-D here. While western blot analysis detected a small population of stable trimers of the fusion protein, chemical cross-linking and SEC-HPLC indicated that the fusion protein was predominantly a trimer. In contrast, purified thioredoxin ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257629 Fri, 13 Mar 2009 03:33:06 +0100 2257629 http://www.medworm.com/index.php?rid=2257628&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275747%26dopt%3DAbstract Authors: Sureshbabu VV, Tantry SJ, Chennakrishnareddy G, Nagendra G Cyclosporin O (CyO), an immunosuppressent cyclic undecapeptide, was synthesized by convergent approach employing Bsmoc-Nmethyl amino acid fluorides and Potassium Salt of 7-Aza-1-hydroxybenzotriazole (KOAt) in solution by stepwise assembly. The couplings were found to be epimerisation free. The difficulty in the coupling of four consecutive N-methyl amino acids at position 8, 9, 10 and 11 was overcome by repeating the coupling thrice at these critical positions. All the ten protected peptide fragments of CyO starting from the dipeptide to the undecapeptide and final protected as well as CyO were isolated and fully characterized. PMID: 19275747 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257628 Fri, 13 Mar 2009 03:33:06 +0100 2257628 http://www.medworm.com/index.php?rid=2257627&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275748%26dopt%3DAbstract Authors: Hu W, Chen X, Yu G, Chen Y, Shen Y, Zhang Y, Gong Y A novel grass carp growth hormone receptor (gcGHR) cDNA was cloned by RT-PCR method. CHO-K1 cells were transfected with eukaryotic expression vector pcDNA3.0 containing gcGHR entire coding region, resulting in a stable CHO cell line expressing gcGHR (CHO-gcGHR). Bioactivity assay revealed that silver carp growth hormone (scGH) bound gcGHR with dissociation constant (K(d)) value of 1.96 nM and stimulated CHO-gcGHR cells proliferation with the sensitivity of 20 ng/ml. The cells proliferation assay was also provided to measure fish growth hormone levels of pituitary and refolded protein. PMID: 19275748 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257627 Fri, 13 Mar 2009 03:33:06 +0100 2257627 http://www.medworm.com/index.php?rid=2257626&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275749%26dopt%3DAbstract Authors: Salahuddin P The acid induced unfolding of HSA (Human Serum Albumin) was studied using UV-difference spectroscopy, fluorescence spectroscopy and far-UV CD spectroscopy. In UV-difference spectroscopy, the molar extinction coefficient decreased from N state to F state. Partially buried Tyr residues are transferred from a medium of high polarizability (native N state) to a medium of low polarizability (F state). This is followed by loss of two electrostatic interactions Lys 205-Glu 465 and Arg218-Asp451 or one electrostatic interaction Lys205-Glu 465 / Arg218-Asp451 and one buried carboxyl group of acidic amino acid. Similarly, UV-difference spectroscopy showed a decrease in absorbance in Fright harpoon over left harpoonleft harpoon over right harpoonE transition due to exposure ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257626 Fri, 13 Mar 2009 03:33:06 +0100 2257626 http://www.medworm.com/index.php?rid=2257625&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275750%26dopt%3DAbstract Authors: Fei X, Zhang Y, Gu X, Qiu R, Mao Y, Ji C Human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9), a subunit of an Elongin C-cullin-SOCS box (ECS) E3 ubiquitin ligase complex, is believed to be involved in specific substrate-recognition for ubiquitination and degradation. In fact, this specific substrate-recognition is determined by the ankyrin repeats of hASB9 protein. Here, we have cloned and overexpressed the hASB9-2, the splice variant of hASB9 with only one ankyrin repeat domain, as a 6His-tagged recombinant protein in Escherichia coli. The purified hASB9-2 protein was crystallized by the hanging-drop vapor-diffusion technique and diffracted to 2.2A resolution. The data showed that the cubic hASB9-2 crystal belongs to space group P4(3)32 with unit-c... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257625 Fri, 13 Mar 2009 03:33:06 +0100 2257625 http://www.medworm.com/index.php?rid=2257624&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19275751%26dopt%3DAbstract Authors: Meng G, Bai X, Green TJ, Luo M, Zheng X A novel human Glyco_18 domain-containing protein, SI-CLP, was detected recently in human bronchoalveolar lavage of patients with chronic inflammatory disorders of the respiratory tract and peripheral-blood leukocytes. The expression of SI-CLP is up-regulated by dexamethasone or IL-4 and involved in the Th2 cell pathway. To further investigate its structure and function will provide new insights into human immunity and related disorders. Here we provide a preliminary crystal image of SI-CLP using the hanging-drop vapor diffusion method. The crystals of SI-CLP diffracted X-rays to a resolution of 2.7 A. The crystals belong to the space group P3(2)21 with unit cell parameters a = b =99.79 A, c =250.53 A, alpha=beta=90 degrees , gamma=120 de... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=2257624 Fri, 13 Mar 2009 03:33:06 +0100 2257624